Well, it's not like that's a thoroughly unknown problem. eBPF (https://lwn.net/Articles/740157/), for example, which effectively relies on running user-supplied bytecode in kernelspace, attempts to solve this (and does it reasonably well) by imposing a couple of constraints on the code you supply. These constraints, in turn, allow the program to be statically-analyzed before running it.

In my experience, 90% of the cases where homoiconicity is useful are cases where the code you execute is trivial enough that you can statically analyze it, for example. E.g. you use the data to generate trivial processing code that would be tedious to write by hand.