Assuming HTC does not want to retire the big maps it is probably easiest just to have a switch from small/large map rotation to just small map rotation at some point in the day. Just have the map for each rotation start in the same position it ended the previous day.
Shutting down some bases on a map during low numbers hours seems like a solution, but it has its complications. The current MA maps are not designed around the idea and it would be hard to select fields in such a way as to be fair to all sides whatever the front line position. Also, what do you do about CVs? Preventing off peak players from using them is not really on.
I vaguely recall HTC trying something like this years ago, they didn't limit which fields you could up at but which fields you could take to just a handful. It wasn't popular with players and was dropped pretty quickly IIRC.
Another possibility is rather than deny the use of bases, just make certain bases more attractive for players to attack. Lets say each base is given a points score on the map, for instance 2 for a port, 3 for a V or small airbase , 4 for a mid, 5 for a large field. To win the war you now have to get X points off the other two sides. Give a handful of bonus bases double or triple or more points score. This would encourage win-the-war types to attack those bases. Also destroying objects at those bases doubles or triples the players' individual scores as well. This then encourages the score-obsessed to attack those bases. The "I-just-want-to-fight-someone" guys are then more likely to find some action at those bases.