According to his ORIGINAL contract (and I assume his extension is worded similarly), they've easily got him for cause if they want to due to his violations of NCAA and/or conference rules. This includes oversight of the program, so "I didn't know" isn't an excuse.
Anyway, under the original contract, the language is basically as long as the "head coach (Harbaugh) remains employed..." in terms of receiving the bonus for achieving whatever result (winning B10, beating Ohio State, etc.). The suspension isn't really covered. They'd have to fire him retroactive to prior to the suspension, which I believe they could do, to avoid paying it.
This assumes, of course, the language wasn't changed in subsequent. The original contract I saw was not particularly well written. I would not hire the firm that wrote it whether I was Harbaugh or UM. Perhaps Michigan law precludes the use of certain clauses that appear to be left out but I highly doubt it.
