I've said this before but it bears repeating: If a timer goes twice as fast, then it's not an accurate timer anymore. A better way to do it is to have neither timer count down unless both points are owned by the same team, and maybe reduce the starting time if rounds end up dragging on too long.
And KOTH in this game should be doable; I'm all but certain the first KOTH map I saw was actually a custom map made before it became an official mode (either that or the HUD entities were added to the game in secret before Viaduct was released, and people figured out how to use them).