I think the whole monkey patching thing is a bit of a red herring, gevent changes the python execution model enough that there may as well be a "gpython" command which runs Python - Python+gevent may as well be a different distribution of Python.
But even so, is the cost of having to run a monkey patch (or some other startup script) greater than the cost of having to rewrite an entire ecosystem of libraries? I don't think so, not by a long shot. Just look at the whole "aiolibs" project to see how ridiculous this has become. Are some of those libraries better put-together than their originals? Sure. Is it worth splitting an ecosystem in half and having one half not even able to call into the other half? Absolutely not.
But even so, is the cost of having to run a monkey patch (or some other startup script) greater than the cost of having to rewrite an entire ecosystem of libraries? I don't think so, not by a long shot. Just look at the whole "aiolibs" project to see how ridiculous this has become. Are some of those libraries better put-together than their originals? Sure. Is it worth splitting an ecosystem in half and having one half not even able to call into the other half? Absolutely not.