The commonly accepted solution, if this is an issue for you, is to run two instances of Emacs: one to edit in, and one to run EXWM. The days of "Eight Megs And Constantly Swapping" are well behind us; one can easily afford to run two (or many more) emacsen. And it can't be that much more bloated than, say, kwin...
If it seems interesting to you or you're experimenting with keyboard-driven tiling WMs, though, I would highly recommend this particular fling.
Been using it for a couple of years, and in practice it does not cause me much trouble, at least not for me.
Can you share more about your particular setup? I use a pretty vanilla setup of Doom emacs on Linux, and while I really wish to give exwm a try my experience with emacs has been too unstable so far. E.g. it sometimes crashes when it gets an I/O error trying to write a file (which happens when a USB drive is removed by accident). A more common annoyance is the entire program freezing while waiting for plugins that should be asynchronous, like Tramp or some LSP servers.