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 increasingly 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.
Zepeda Patterson also mentions that the army has it out for Marisela Morales, partly because she's a woman. When Calderón decided to lean more heavily on the army, the push-back typically focused on the potential for human rights abuses and the danger of corruption in what had become one of Mexico's more honest institutions. These were, not coincidentally, the most immediate negative consequences. But, as I probably did not give enough attention to at the time, having the army involved in such a politically sensitive issue sowed the seeds for deeper conflicts regarding its role, which, according to Zepeda's version of events, are manifesting themselves in the Hank case.