Things like Cython are great until they aren't, so yes, I think of them as a stop gap (albeit a practical and useful one). Any time you change interpreters or the execution model, you risk compatibility challenges with third party libraries and native modules. You also risk getting painted into a corner by their limitations. They definitely can help with hot code paths when their trade-offs don't prevent it but it still ends up being a kluge working around fundamental language issues.

But when Cython fits, it's great, and a good tool to have in your toolbox if you're working with Python.