We've solved this problem by breaking our architecture up to be more distributed and introducing Python 3 one small service at a time.
Same here. It's also been a great opportunity to step back and reevaluate some early-startup engineering decisions that've made the new service codebase fun to work with. Rather than having a single backend that has to handle all possible situations ("this one thing we're talking to speaks XML..."), we can only deploy the stuff actually needed for that one service ("I think we can safely assume all-JSON here"). I highly recommend this approach.
If you cant evolve a system incrementally because of excessive coupling, that's a problem, sure, but not a problem of either the platform you are on or the one you might be thinking about moving to, unless the former forced a tightly-coupled architecture on you.