The only sorts of companies where server costs could increase hugely due to a sudden need for hardware isolation are those where they're running tiny or incredibly bursty workloads. Big companies like Netflix that use tons of cores can just binpack their work all together on the same hardware so their jobs only share hardware with other jobs controlled by the same company. Effectively, cloud providers will start offering sub-clouds into which only your own jobs will be scheduled.

This is actually how cloud tech has worked for many years internally. I worked at Google for a long time and their cluster control system (Borg) had a concept called "allocs" which were basically scheduling sub-domains. You could schedule an alloc to reserve some resources, and then schedule jobs into the alloc which would share those resources. Allocs were often used to avoid performance-related interference from shared jobs, e.g. when a batch job kept hogging the CPU caches and slowing down latency sensitive servers. I suppose these days VMs and containers do a similar job, though I think the Borg approach was nicer and more efficient.

I guess this sort of per-firm isolation will become common and most companies costs won't change a huge amount. The people it'll hit will be small mom-and-pop personal servers, but they're unlikely to care about side channel attacks anyway. So I wouldn't sell stock in cloud providers just yet.