In the normal CTF barely anyone does the objective, and the Arena mode will make it even less objective-focused. In the normal Arena, control point exists just to stop people from hiding all around the map; this means that CP of the map is not the primary thing. But since your concept tries to make flags the primary thing, that'll lead to more split teams and more useless deaths; so that will make players realize that there is no point in trying to win by objective and they'll just continue the deathmatch
All of this was assuming that you'll do typical CTF map with caps on opposite corners of the map. But here's what I can suggest: place an enemies' flag really close to spawns and make the cap area somewhere in the middle of the map closer to enemies' area. That will actually reward risky teams with more kills and will encourage players to play more mindful to not let the cap happen on the opposite team. Though, my guess is that it'll be hard to make this work good
Let me know if you'll actually want to make this kind of map, because if you don't, I would really love to try making it!
