CocoonJS should either support everything, or at least do nothing (and not crash) if you use an unsupported feature. I think all the official plugins and behaviors should work, except for the Text Box and Button form controls. The main problem is third party plugins and behaviors which can use any code and may use features not supported by CocoonJS.
If you find anything that is crashing CocoonJS, check the console for errors and let us know what they are, as well as the list of third party plugins and behaviors you're using. At the very least it should be possible for Ludei to prevent it crashing and ignore the call instead.