Regarding using the repeater input as a control frequency... Set it to require a control operator action to bring it back from the 3-minute timeout. That would solve the jammer issue. Just use your own transmitter to make sure it times out, then don't reset it till the trouble has passed.
I had a macro in my 7K I could invoke if I had to be away from town, that would do this. Many early ham repeaters in the Buffalo, NY area, where I got started in ham radio, were configured this way, even when they did have alternate means for control. If I recall correctly, it may have been an FCC requirement in the old days that a timeout not auto-reset when the carrier dropped. 73, Paul AE4KR