I think we do take care of shows that are not recorded to completion if you choose "Do not record programs that have been recorded in the past" (though I have to double-check on that).
However, if you turn on "do not record rerun", then MC will not record it again. What constitutes a rerun? If the guide says so - depending on the source of guide, you may get a flag that says "previously-shown", or you get an "original date". In case of latter, a show presented more than once on the same day may actually be recorded more than once (if the original date is not in the past of course).