I think it might be better to think of purity as a way of ensuring that performance and logical correctness are independent effects. Purity allows us to safely improve performance by making local substitutions of faster but logically equivalent code, without having to reason globally about correctness. It's also what allows us to tolerate variation in performance (within reason) without threatening correctness.
For crypto we can reason separately about logical effects (does the crypto work) versus information leakage. For a user interface, we can treat dropped frames as a performance problem rather than a correctness problem.
This is useful even though we still care about performance. Substituting a much slower function for a faster one probably isn't okay, but purity lets us understand the effect.
I find any single effect is easy to reason about in isolation, it's the interaction that gets tricky. Viewing purity as isolating performance is just one perspective on this - you can equally view it as isolating state mutation, or isolating async transitions.
You can look at const correctness in C++, Java checked exceptions, async versus non-async functions [1], and Rust's ownership model as other examples where making fine distinctions for good reason has a side effect of making substitution harder - or perhaps safer, depending on your point of view.
If you need it, you need it, but when you don't, it's a luxury to be able to substitute whatever you like and see what happens.
[1] http://journal.stuffwithstuff.com/2015/02/01/what-color-is-y...
I think this is avoidable if your types/effects can decompose properly into orthogonal factors. E.g. with a Future type and a generic monad abstraction it's fairly easy to substitute a sync call for an async call - you have to be explicit about the change you're making, but only very slightly, and you'd never get confused between changing sync/async and changing the "actual" type that's returned.
From an operational perspective a good definition of equivalence would be very difficult. E.g. if your language allows making system calls there are dozens or hundreds of those with no real model of how they interact, so it's very hard to say when one sequence of system calls is equivalent to another. Possibly the most natural notion of operational equivalence is to say two programs are equivalent if they execute the same sequence of CPU instructions, but that would mean that nontrivial programs were virtually never equvialent to each other, even if they both just printed the same string.
Equivalence: unification of types (can't make I'll-typed substitutions)
Output only effects: have your language define only one such monad
About to depart on a flight, so can't elaborate further.
Of course this means "pure" is not an absolute term but rather relative to a given definition of "equivalent". But this isn't circular and is practically useful: if you're working in a context where precise execution time matters (e.g. cryptography) you really do need to use a different concept of "pure" language from what you would use in a more "normal" context where two programs that produce the same output are equivalent even if they take a different amount of time to execute.