brent rmo and dc gets rid of some stuff. But eopkg in no way gets rid of an app's folders in .config, .local, etc etc.
That's right. Eopkg won't touch anything in your home directory.
I'm not sure where the "etc etc" folders are, but for the stuff in your home directory, it takes only a few seconds to turn on "show hidden files," then find the folders named "Nautilus" and rm -r
them at their top level.
But as @stalebrim pointed out, with Nautilus removed, nothing will be looking for them so they're as good as removed even if you don't bother to do that. And it's only for (we're hoping) a short time until 4.4 .ISO files are released.