The problem is that there is only a small minority that think the way you do. MOST players play the game to win the war. Making that harder will only drive those players away instead of create more action as they LOL!!! "fight" for those bases.
I think the biggest issue with people logging off on a map win is just because its time to. Many a time I would set a time to log and go blowing past it because we only needed a few more bases for the win, and next thing you know Im off to work with only 2 hours of sleep if that! LOL!! those were the days. The other issue is that "terminal action count" is. There is a certain number of players that when reached the areas becomes fun and full of action. Getting to that number after a reset is just that much harder with players logging.
Give everyone who logs back in and stays for 5-10 minutes 15-25 perks. If they push that hard for the win perks, maybe they will come back and hang around for 10 minutes.....and get hooked again for some easy perks.