Issue is not having military officers anywhere in a ministry, this is the norm here, military officers are posted in other ministries also where the govt requests for such personnel. issue is policy making, State Deptt makes policy in consultations with Pentagon, and where Pentagon has no interest, State Deptt toes that line. So even US Foreign Policy is in some ways and in some matters controlled by the Pentagon.
Army speaks in the foreign policy where it is essential like in case of India, US etc etc, just like what Pentagon does. In the recently just held CBM related meeting lead by foreign offices of India & Pakistan, an Indian Army Brigadier was part of the delegation plus other armed forces personnel too, thus even Indian officers are send and included in Foreign Affairs.
And yeah our Army may be taking too much part in these issues, but that is due to certain factors, MOFA is making its own policy with respect to lot of other things but in certain critical issues, Army has to come into play, that is due to regional issues and the immaturity level of our politicians.
So, defence forces taking part and influencing foreign affairs of their respective countries is not limited to Pakistan,, super powers do that, so do 3rd world countries. So no need for you to make a fuss with respect to Pakistan or may be its what you are for on this forum, to create fuss about non fussy issues.