That sounds like a rather extreme step. Even if you never use your moonroof (I never either, opened it for the first time in years recently and noticed the rust), the right and safe thing to do is to take it apart, treat the rust (wire brush, rustoleum) and then reassemble.
I am not 100% sure yet, but if you see my post above, it seems there is a way to take apart the frame and glass even if your motor is jammed, treat it and reassemble. Replace any worn weather striping while you are at it.
Covering up the problem with silicone will only make it worse in the long run, and any necessary fixes extremely hard when you do need to address the problem.