Based on Zuii's statistics, The V-1 could be programmed by a targeting system where you have to enter in the right numbers to get it reasonably within the ball park, like the german rocketeers did back in WW2. A player would have to figure out a flight plan (ex. Distance to target from launch base, amount of fuel needed, warhead size, target altitude, etc.) and enter it in to the targeting system. then all he/she would have to do is "fire and forget", but this way it makes firing a V-1/V-2 very challenging and along with being a perk vehicle, more delibrate to fly.
Maybe making it so you could only fire one at a time and you had to wait in the tower until it is destroyed would help keep the targets reasonably close to the launch base and swarms of V-1/V-2's out of the sky.
BTW, if the V-1 had a level flight speed of 350-400 mph shouldn't that be faster than any plane could possibly catch it? I guess diving in from above it or making a lucky HO pass is the only way to destroy it from the air. And if I remember right from the History channel it was near impossible to hit from ground fire either. Somebody correct me if I'm wrong.