the LabVIEW Run Time Engine (RTE) isn't related to GPIB (VISA?) driver. If you have a utility that uninstalls one, then run it again and point it at the RTE.
The uninstalled piece may have a dependency and prefer that you uninstall one of the two parts first (I forget if these two are tied together). If they are, then you should unistall the 488.2 part first.
here is a link that describes some of the process (silently uninstall). It is written for IMAQ, but the process is the same.
let me know if you have any problems.
Joel