Ethan-
No RTV...there are some pretty specific applications that it is good for, and this is not one of them. Fix the problem instead of adding a band-aid. Make sure the cover is straight and flat, remove all gasket residue from the cover and transmission housing, and if the bolt holes in the cover are indented from the bolts being overtightened, use a ball peen hammer to flatten or even slightly dent them to the outside of the cover, and use a new gasket. If you are still worried about it leaking, use gasket sealer, not RTV. RTV is not gasket sealer.
I have seen everything from valve cover gaskets to tires (seriously) "sealed" with RTV. Had a KT-17 that had probably 5 minutes on a rebuild that threw a rod into the cam because a giant glob of RTV got stuck in the oil gallery in the crankshaft. People just love to put that stuff where it doesn't belong, or use WAY too much in places it does.