I don't think a large map is necessarily a bad thing. It has its disadvantages but also upsides. All of my map ideas (including the finished one: http://www.teamfortress.tv/35172/ultiduo-sacred ) have been quite large. This naturally means that it takes longer for the respawning team to come out of spawn and move forward to the point or wherever the other dudes are holding. The way it seems to work on all ultiduo maps is the team that doesn't own the point respawns damn near as instantly as possible while the team that does own it is a bit longer (maybe double?) which allows the attackers time to stand on the point and cap after killing the defenders.
I would see just how short you can make the respawn timer for the team who does own the point. If it's so short that they can quickly come out and defend the point from the attackers capping then it might be too short. If there's no such issue then you should be good. Basically make them all as short as possible and adjust from there imo...