Previously side channel attacks like this have been seen by the security community as unreliable things which only work in very specific cases and have to be averaged over millions of runs.
This attack shows a side channel which is general purpose, reliable, and fast.
There is no fundamental reason why speculative instructions should be allowed to mutate the cache.
OTOH the contention-based side channel attack on speculation has been public knowledge for over a decade. [1]
[1] Z. Wang and R. B. Lee, "Covert and Side Channels Due to Processor Architecture," 2006 22nd Annual Computer Security Applications Conference (ACSAC'06), Miami Beach, FL, 2006, pp. 473-482. doi: 10.1109/ACSAC.2006.20
There is: hundreds of instructions can be in flight speculatively at the same time, especially if you take hyperthreading into account. Good luck rolling them all back.
The question is not whether the cache should be mutated during speculative execution. It's what kinds of speculative execution are allowed, and in some cases it's not even clear if fences should be placed by the programmer (whack-a-mole style), the compiler (not sure how) or the processor (probably not). It's non-obvious enough that how to solve it is to some extent a research problem.
The point of VIPT caches is exactly to use data before all the checks are completed.
It's easy to judge the sanity of things ex post, but maybe it's not that easy if it took 20 years to find the issue.