You could get rid of jemalloc, but on the other hand you could also just compile it with -fembed-bitcode. (It's part of the Rust standard library, so that's a bit more work. Rust code doesn't have this issue because .rlibs contain serialized ASTs, and passing -C lto makes rustc only use that rather than use the precompiled bits. In any case, it's just a matter of rebuilding.)
Incidentally, I just tried updating my nightly Rust, and it stopped working - clang started failing to read the bitcode, bailing out with a vague "error: Invalid record". This is not too surprising, because Rust just landed a big LLVM upgrade two weeks ago. Newer LLVM can read older bitcode files but not the other way around, and even though LLVM 4.0 was released months ago, Apple seems to only sync with trunk yearly, along with major Xcode releases. (You can tell based on the --version output.)
However, Rust can be built against an external LLVM (rather than the fork it uses by default), and AFAIK it tries to preserve compatibility with older versions. So it should still be possible to use the latest rustc, you just have to compile it yourself against a slightly older LLVM.
I wonder if the dependency on jemalloc can go away once custom allocators stabilize. Then the macOS system allocator could be used.