For now, each process runs many isolates - but a single server run many processes. Cloudflare have implemented a similar mechanism [1]:
> Workers are distributed among cordons by assigning each worker a level of trust and separating low-trusted workers from those we trust more highly. As one example of this in operation: a customer who signs up for our free plan will not be scheduled in the same process as an enterprise customer. This provides some defense-in-depth in the case a zero-day security vulnerability is found in V8.
[1] https://blog.cloudflare.com/mitigating-spectre-and-other-sec...
As long as you run each customer in a separate OS-level process, you should be good. But then, that is not much different from Lambda or other FAAS implementations.