As for MvM really being CTF, yeah, that's been obvious since the start. When MvM first launched, you'd always see the regular CTF HUD before the client realized you were playing MvM and changed it. Also, TF2 only has 5 core "game types:"
0 = Unknown (used only on Training maps by Valve)
1 = CTF
2 = Control Points
3 = Payload
4 = Arena
All other types are based off of those.
Yeah but all of that can be fixed. That mod was just quickly made.
I don't really do TF2 plugins any more, but couldn't you just do a skin override instead? Although you'd also have to do skin overrides on any cosmetics for that player, too...