Not a good idea. I did something simlar to this with my original Droid. Here's the thing. If your replacement launcher gets screwed up, or if you uninstall it, you have no way to do anything; such as get into a file manager to reinstall the stock launcher. It's not hurting anything sitting in the background.
What would be the difference from what you are experiencing now to deleting the stock launcher. Just a sense of cleanliness, know it's not there?
Samsung Galaxy Nexus (VZW)