Contrary to the opinions held in some circles, military leaders tend to be very conservative about the use of force, because they understand the risks better than civilians. In that sense, the concerns about the number of generals in the cabinet is unfounded.
While Flynn is a notable exception, you can expect the military, as a whole, to push back on torturing suspected terrorists, and they will object to establishing any kind of unholy alliance with Russia. His comments during the campaign notwithstanding, Trump is likely to show some deference to the leadership, so there is some doubt that he will ultimately establish the kind of relationship with Putin that he so obviously desires.