RootExplorer, Astro, and ES File Explorer all support multi-select. I personally use RE, and ES to delete files out of the sysdir. You dont really have to close program (although it doesn't hurt), the deletion forces the file to close. I wold recommend a reboot after removing any sysdir files though (you may get a few Forcecloses if not).
Titanium Backup also can remove any files from the sysdir, and you dont have to mount (it automounts). unlike ES and RE where you have to manually mount at least once. but you dont get the option to multi-select. The interesting thing is you can "freeze" with TB, which is like "deleting" without deleting to see if any issues arrise. I believe this is the same function if you were to just rename the .apk extension to something like .apk.bak (which kills the file from being able to run) to test if it causes issues, then later you can delete.