If an air fleet intercepts another air group, there is one combat before the attacking fleet does its mission. If the attacker loses 1-2 factors, it still does a majority of the damage it would normally do.
Why don't interceptors also disrupt the attacking mission? Many bombers abort that weren't actually killed. A different way to handle it: For every 2 factors of interceptors, 1 factor aborts after combat. So if a 10-factor bomber attacked a target, was intercepted by a 10-factor air fleet, and the bombers lost 1 factor, only 4 of the surviving bomber factors would attack the target (with the other 5 aborting due to the interception).
With the current system, there is little incentive to intercept - especially when the German air is so much more effective due to advanced aircraft and HQ.