Hi FoodStuffs, don't get your hopes up my answer might not be what you want to hear, I have had a sort of similar situation with the military and the Rookie camp.
I had taken a quest to assassinate someone in the Dark Valley (this is quite early on in the game about 10 quests in) and I completed the task well with minimal casualties and those were bandits, so I make my way back to Cordon via the Dark Forest; a few bad chickens=pseudogiants and blowout later but nothing too bad, so back through the tunnel OK and now to sneak past the car-park and the bandits there OK.
Back at the Rookie Camp and I find the NCP who gave me the quest and received a SIG-5?? (a gun) and the best gun I had to date, I also was carrying loads of loot, 4 pseudogiant eyes.. they fetch a lot of RU's so to find a talking NCP to trade with and off load, then BAM! snipped from behind by the damn military... bugger I thought, better be more careful next time so I F9 for quick load and damn me it happens again but this time it was with 3 or 4 military, the next thing I know I have the entire garrison descend upon the Rookie Camp all determined to send me to quick load hell!, NONE of the Stalkers/Loners or anyone in the Rookie Camp was even half aware the the military was using their camp as a battle ground and I hid in Sid's bunker only to hear grenades going off left, right and above, I would pop my head out occasionally only to get it shot off from someone the other side of the camp... this went on for an hour with over 50 quick loads, all the expendable rookies were dead and the disgruntled groans from Wolf and Nimble as the took yet another grenade was too much and I did the only thing left I could think and loaded back into the Dark Forest and came through the tunnel again, I then went to the Swamps to fulfil another quest I had also taken and then came back to the Rookie Camp to find... no military at all and peace had returned.
you might be lucky and find no military at the bar if you can load a save point before you entered the Rostok map