When speculative execution (and caches) were invented and put into widespread use, no one thought about timing attacks, nor was the practice of running untrusted code on one's own machine common.
Doesn't multi-user timesharing and virtualization predate every modern CPU and OS though?
At first, computers were very expensive, and so were shared between many users. Mainframes, UNIX, dumb terminals, etc.
Then computers became cheap. Users could each have their own computer, and simply communicate with a server. Each business could have their own servers co-located in a datacenter.
Then virtualization got really good, and suddenly cloud servers became viable. You didn't have to pay for a whole server all the time, and if demand rapidly increased you didn't need to buy lots of new hardware. And if demand decreased you didn't get stuck with tons of useless hardware.
The second stage (dedicated servers) was the case when speculative execution was implemented. We're currently in the third stage, but Intel haven't changed their designs.