I can see two major problems:
1. If they can't be raised until the last 2 minutes of the match, it doesn't actually change anything - most battles are won before there's 2 minutes left.
2. This just creates an area where everyone bunches in to "secure" the flags. Makes them a sitting duck for archers and cavalry, thus intensifying the problem.
Solution:
Several flags across the map which raise and lower depending who's there. Once a flag is raised, it stays raised until an enemy starts to cap that flag point. The team with the highest flag on each point is awarded the difference between their flag and the opponent's flag (in decimal), each of the flag sets scores are added up and whoever has the most wins - or whoever wipes out the enemy team.