By having the linker work on hashes of implementations you eliminate that problem but create a new problem. You can no longer change the behavior of the function because you can't change the function. That means you can't suddenly change behavior that some caller is counting on, but it also means you can't fix bugs without changes in the caller.
Maybe the simplest solution is to allow the function to change to the new version, but make it easy to revert in the event that something breaks. This of course means that you can't make the names of the functions their hash (without lying, preventing the runtime from checking that hashes ways match, or modifying emitted bytecode or native code to do what you want), it has to be an orthogonal layer on top of them like types (as I mentioned elsewhere in the thread).