Mutating argv is fine for how it is usually done. That is, to permute the arguments in a getopt() call so that all nonoptions are at the end.
It is fine because it is usually done during the initialization phase, before starting any other thread. setenv() can be used here too, though I prefer to avoid doing that in any case. I also prefer not to touch argv, but since that's how GNU getopt() works, I just go with it.
Once the program is running and has started its threads, I consider setenv() is a big no no. The Rust documentation agrees with me: "In multi-threaded programs on other operating systems, the only safe option is to not use set_var or remove_var at all.". Note: here, "other operating systems" means "not Windows".