Instead of modifying the AOSP make files (which is annoying because then you need to track your changes) it is easier to add a LOCAL_OVERRIDES_PACKAGES line to your app's make file.
For instance:
LOCAL_OVERRIDES_PACKAGES := Launcher2 Launcher3
added to your Android.mk file will ensure that those packages are not added to any build where this package is added.
Following that, you should do a
make installclean
and then start your build the same way you always make your build. The make installclean is important to remove the packages that are left behind by the previous build.
I also just found a nice answer to how to do this in another question, see: How would I make an embedded Android OS with just one app?