mil law

i am an army officer (short service) and plan to leave army this year(i had taken extension for two years).Last year in May my cousin visited the city i was posted in where he got into a fight with a DSP(that officer was talking to him the way policewalas generaly talk to the youngsters and they ended up hitting each other). When i tried to intervene, he(the DSP)got even more angry and filed an FIR against my cousin and i (saying that i was in my uniform and threatened to SEE him if he didn't let my brother go. Now my problem is that in order to leave army i have to put up my papers and i want to know if this case can create any problems for me in getting the clearance from the army offices(as they are in picture of my case). i am still trying to smoothen out thingswith tha police officer outside but that might take time while iwant to leave at the earlist .Please guide me as soon as you can.