The problem is that programs can be entire systems, so "doing it at the system level" still means that you'd have to build boundaries inside a program.
you can use OS apis to isolate the thing u want to use just fine..
and yes, if you mix privilege levels in a program by design then u will have to design your program for that.
this is simple logic.
a programming language can not decide for you who and what you trust.
For the sake of the argument, what if I wanted to isolate numpy from scipy?
Would you run numpy in a separate process from scipy? How would you share data between them?
Yes, you __can__ do all of that without programming language support. However, language support can make it much easier.