...I think disabling flag dropping is an okay idea.
It's an objective game so you need to protect the flag carrier. There's no need to when he can fight just as well as anyone else on the team by dropping the flag. While the objective is moving, the other team should enter a fight with some advantage to have a chance at stopping the capture.
It could all be totally fine, there are just a bunch of weird tradeoffs being made that people are naturally apprehensive toward. You give the flag carrier a (pretty weak) weapon, but he can't switch away from it. You make the flag carrier faster, but then you broadcast his location to everyone in the match, making him an immediate target. I mean, you always needed to protect the flag carrier, whether it was through direct intervention and killing his attackers as he's being attacked, causing a distraction on the other side of the map so he can sneak away from it, or by spawn trapping people so that their pursuit options were limited. The carrier was always gonna have a few shots on him by the time he dropped the flag and turned around, making him an inherently weaker combatant because of his importance. Teamwork was always required. Now, with that waypoint that you can't escape by dropping the flag, some of those options are now limited.
Take a CTF game of Sanctuary or Asylum. Enemy grabs the flag, they take it one of four or five routes. The defenders, who have been outplayed and have lost their flag, needs to intuit which of the routes is the most likely for him to take immediately as they spawn and move to cut him off or hit him in the back. Now, it tells you exactly which route he's taking. There's no guesswork, and less map knowledge required. You're still requiring teamwork, but that definition is a little more strict.
I have no idea if it'll be great or terrible at this point, but without playing it? I'm not a huge fan, because of
the combination of the waypoint and glue on the flag pole.