I'm having the same problem. Why can't I turn off those waypoint indicators?
The way CTF is set up now is seriously poor; I can only create ONE style of gamplay. That's not Halo. Halo has always been about creating the gametypes for exactly how you and your friends want to play! But nope, now I'm stuck playing a CTF where the two teams just compete to see who can score a flag the fastest. There's no point to taking an alternate route and being sneaky, no hunting down the flag carrier, no strategy, no team-coordination, not even returning the flag.
Seriously, without being able to disable that waypoint icon, the CTF in this game is broken.
I also think there should be an option to set it so the flag carrier can either use a pistol, use no weapons, or use all weapons. And turn the grenade button into a flag-drop button.