Root and then unroot afterwards?
Absolutely. Well...almost. Just make sure you set the partition from rewritable to read-only once you're "unrooted". However, once you are unrooted, binaries like su and the SuperUser apk will in all probability removed, so you will in effect be dropped to a lower privilege level. This will have the side-effect of having the apps installed in the system partition as being uninstallable.

A workaround is to remove/uninstall apps from the system partition, remove root and then add the apps as user apps - this will ensure that they can be updated in the future without the need for root.