Just an idea: instead of using fighters as surrogate turrets, how about waiting to the _end_ of the Ordnance phase to determine which ordnance is removed?
For example, in my turn, I'd move my bombers onto your cruiser, you'd move your fighters onto the bombers, then we'd remove bombers, then you use turrets, then my bombers would attack.
This would give you the chance to intercept bomber waves even at very close range, but would it make it too hard to use bombers? Harder than having cruisers "loaded up" with four fighter squadrons, giving the bombers D6-6 attacks?
Any ordnance that is "intercepted" can't then move in that phase, so if I had fighters in the above exmaple I could move fighters onto your fighters, then move my bombers, then you'd move only your unengaged fighters, then we'd resolve. This still gives some benefit to moving your ordnance first in your own turn. Doesn't seem to encourage mixed F/B waves though... :-)