Jorge Zepeda Patterson, a usually well-informed and reasoned columnist (and academic), proposes two hypotheses why the army launched the raid against Jorge Hank Rhon. Both assumes that the army acted on its own, yet one is considerably more sinister than the other.
1) The army was convinced of Hank's guilt, and launched the operation to catch a bad guy, with the intent also to shore up its increasinly tattered image (particularly compared to La Marina).
2) The army intentionally set out to bungle the operation, a la the Michoacanazo, in order to discredit the PGR, PAN, and President Calderón.
Definitely among the more interesting speculations around the botched operation - though exactly that, speculations.