Spectre/Meltdown ONLY is an issue if you run some untrusted code on your system. If you avoid this, there is not problem. Yes, we like to be able to run untrusted code (such as in a web browser / javascript), but that is not the fault of a car manufacturer that you like to pick up hitchhikers.
Yup, this will hit the EC2/etc users hard, but those people have already IMHO given up on absolute performance by putting themselves in shared environments where bad neighbor syndrome can already hit their perf pretty badly.
But for whatever reason (probably because its easier) the current plan just seems to be to use the big hammer.
Your idea of black/white listing processes might bubble up as a solution in some scenarios. Perhaps it could be pledge-like; if you're savvy enough, try implementing it, or fleshing out the details.
This whole thing is the equivalent of discovering that if someone throws enough nails on the road your car will blow a tire, spin out of control and kill you. With the kneejerk reaction of trying to fill everyone's tires with concrete to avoid the tires blowing out rather than trying to figure out how to keep people from throwing nails on the road (with the idea that spiteful users are more likely on toll roads) in the first place.