Editions are not lock-in; the entire point of the edition system is to allow the version of Rust that exists in 2032 to compile every prior edition in the same project at once, and only single crates at a time have to be 2030 edition.
Before making any change that could possibly be breaking, the change is tested on every single crate on crates.io, as well as on a great many GitHub repos that aren't, in order to make sure there aren't any regressions (referred to as a crater run).
You are right that the problems you describe would be problems if Rust was implemented the way you're implying. That is why Rust was not implemented the way you're implying, but rather implemented specifically to avoid these problems.
The way you describe yanking also seems a bit confusing. If the original project had a dependency that was yanked for security concerns, then the original project was already compromised in the first place. Even then, assuming the lockfile was checked in, then it should still be possible to download the yanked file (plus the compromising code, although the act of downloading a yanked file produces a warning, I believe). If you mean that the project was working fine (no compromise) and then a later version of the dependency was compromised, then no changes are needed at all - the lockfile will always ensure the exact same version is downloaded.
If you genuinely think you've found a situation that isn't solved by the edition mechanism, or by the judicious use of lockfiles for all projects, then I'm sure the Rust team would love to hear it (although I can't speak for them). But from what it sounds like, you're describing issues with the Node ecosystem and assuming they also apply to Rust, despite a number of differences in how the two ecosystems operate.
There’s no downside beyond “it requires development time and maintenance” like any other feature.
I don't have a single, definitive, clear solution -- as pointed out by others -- nobody does. It's not a simple problem.
That doesn't mean that steps can't be taken to improve the situation, perhaps dramatically in some cases.
1) Enforced MFA to publish a crate -- credential theft is semi-regularly seen as an attack vector.
2) Strong links between the "source ref" and the specific crate versions. An example of this done super badly is NuGet. All of the hundreds (thousands?) of Microsoft ASP.NET packages point to the same top-level asp.net or .net framework URLs. E.g.:
https://www.nuget.org/packages/Microsoft.Extensions.Configur...
Links to "https://dot.net" as the Project Website, and "https://github.com/dotnet/runtime" as the repository. This couldn't be more useless. Where is the Git hash for the specific change that "7.0.0-preview.4.22229.4" of this library represents? Who knows...
3) Namespaces. They're literally just folders. If you can't code this, don't run a huge public website. This is more important than it sounds, because wildly unrelated codebases might have very similar names, and it's all too easy to accidentally drag in entire "ecosystems" of packages. Think of the Apache Project. It's fine and all if you've "bought in" to the Apache way of doing... everything. But imagine accidentally importing some Google thing, some Netflix thing, some Apache thing, and some Microsoft thing into the same project. Now your 2 KLOC EXE is 574 megabytes and requires 'cc', 'python', and 'pwsh' to build. Awesome.
For example, in ASP.NET projects I avoid anything not officially published by Microsoft and with at least 10M downloads because otherwise it's guaranteed to be a disaster in 5-10 years. Ecosystems diverge, wildly, and no single programmer or even a small group could possibly stitch them back together again. Either it's a dead end of no further upgrades, or rip & replace an entire stack of deeply integrated things.
4) Publisher-verified crate metadata / tags. You just cannot rely on the authors to be honest. It's not even about attacks, it's also about consistency and quality. All crates should be compiled by the hosting provider in isolated docker containers or VMs using a special "instrumented build" flag. Every transitive dependency should be indexed. Platform compatibility should be verified. Toolchain version compatibility should be established for the both the min and max range. Flags like "no-std" or whatever should be automatically checked. CPU and platform compatibility would also be very helpful for a lot of users. The most important one in the Rust world would be the "No unsafe code" tag.
This would stop "soft attacks" such as the guy spamming C++ libraries as Rust crates. Every such crate should have been automatically labelled as: "Requires CC" and "Less than 10% Rust code".
Similarly, if a crate/package changes its public signature in a breaking way, then the publishing system should enforce the right type of semantic versioning bump.
Essentially, what I would like to see is something more akin to a monorepo, but not technically a single repository. That is, a bunch of independent developers doing their own thing, but with a cloud-hosted central set of tooling that helps gain the same benefits as a monorepo.
I'm expecting a lot of arguments along the lines of "that sounds like a lot of work, etc..." Meanwhile Mozilla had a large team for this, millions of dollars of funding, and did not do even 0.1% of what Matt Godbolt did in his spare time...
Or even better, make crates request permissions for what kind of functions they can call, similar to the chrome plugin API. A graph crate doesn't need encryption, file opening or netstack permissions.
Someone could always roll their own IO, but self reporting and automated detection tooling (to catch those that slip through the cracks) would bring this percentage way down.
Maybe the language could even evolve "unsafe" for IO, even if just as a flag for users. That way it would all be incredibly easy to audit.
Refactoring breaks everything - just look at Python 2 to Python 3. Part of the problem is having a bill of materials and having accurate tracing of the ingredients of a build, such as reproducible builds. But the time investment in these is hard work.
Computers are good at cross referencing. If you indexed everything in a graph database. It should be a simple graph Search to find dependencies of a git commit hash, binary sha256 installer file. And a web of sha256 relationships. And mapping between them and commit shas. It would be useful for security too but also interested in things being robust and reliable. Like you say it's a monorepository but not one.
Tooling is what's needed
The python packaging experience and ruby bundler and npm and other version manager experiences simply leads to common breakage.
A common following-up question the Haskell people used to say when that was being discussed there is, if your build system can do that, why do you need semantic versioning for?
Still, it's better than doing nothing. There's nothing similar to Stackage or Backpack on Rust, so it would be a clear gain. It's just that you can go further.
It's inevitable that the conclusion will be the same if the same steps are taken in the same direction. The counter-arguments fail to recognise the special case of "most of us are from Mozilla and we all get along[1]", "no-one has attacked us yet so no-one ever will[2]", "it's tracktable to untangle the dependency hell in your head because there aren't that many crates (yet)", and of course "we all know this history like the back of our hand, because we've all been around since v0.1 alpha."
I'm picturing "10 years later" when some junior developer at MegaCorp Inc desperately tries to figure out why the legacy Rust 2018 version he's forced to use in 2032 can't compile some privately hosted crate that's needed for an enterprise project. It'll probably depend on a specific version of a crate that was yanked because some transitive dependency had to be yanked because that guy was a Russian kid that sold access to this popular crate for $500 to Israeli spies. Of course now the patched crate requires Rust 2030 or whatever, breaking fifty seven of the two thousand transitive crates being pulled it, so good luck to him with disentangling that mess and making this work.
PS: I wish I was making this story up, but I basically just changed Angular to Rust for a real thing that happened to me, like... a month ago. There is no fundamental difference to how Rust does packages, it's just younger so the mess hasn't accumulated to Angular's levels of madness. Give it time...
[1] Except for that spat with the core team.
[2] That we know of. Ignore the guy spamming popular, single-word crate names and shovelling in 99.9% C/C++ code with the thinnest possible Rust wrapper. Surprise! Your code is now more C++ than Rust.