But you risk a brick, or the system behaving badly, if you do so. You should have a ntrboot capable flashcart handy in case it doesn't go well, so you can reinstall it.
Restoring with GodMode9 won't get rid of CFW, but if you can restore a NAND backup from before you installed CFW (or right after before you installed anything else) and THEN uninstall, then you'll be safe from bricking due to uninstalling (all your system titles will be ok and not depend on CFW to run).