@bilalahm. The story is hard to believe. First of all tokes are not deposited in banks but in post offices. Second, if you have Islamabad registered car and reside in any other city, you can send the book and money to your friends and relatives in Islamabad to pay the token if you are not able to come yourself.
Alternately in every GPO, there is counter for federal taxes and Islamabad token can be paid there.
My uncle who used to live in Multan had his Accord registered in Islamabad as after a road robbery incident he changed his car's number. He used to TCS reg book and we sent it back after paying token here. Simple. (It was when Isloo reg was not restricted as it is today)