It was actually the right decision. If they don't get the miracle, you aren't even raising that point.
Actually I brought that up with a friend of mine, when he called the timeout.
Not because of the miracle play, but like EasyMoney stated, best case he has like 2 or 3 plays left from deep in his own territory (and those would also have included the risk of turning it over in their own territory, if they had gone that route). WISC got unlucky on that final play, granted, but without that timeout MICHST has one set of downs left, maybe even less, certainly not two.
And since they didn't get much pressure on the opposing QB and they were completing a bunch of short passes with ease, there was a far higher chance of MICHST converting around midfield with extra time left and a kicker, which is one of the better ones in college football.