If the other team already reaches 50, no. The rules for a CTF map are, first team to reach 50 points, or until the end of 20 min's.
I guess you could put it this way: Give flag bonuses for the end of the match, HOWEVER, as CTF goes, the first one to reach 50 wins, no matter what flag bonuses give, since reaching 50 first is one of the main goals for CTF.