Ive actually given this a good bit of thought since the game come out...and I actually agree that bombardment shouldn't be lethal, as that would allow artillery a primary role in ground combat.
Thing is I dont view bombers as artillery and I think they should be different. The main problem is the game views them as bombardment and nothing but fighters on air superiority can really attack back, so if they was lethal they'd be too powerful.
Here's how I think bombers should work personally, but I doubt even part of this happens even as an editor option for mod makers
Air vs Air in civ3 works fine as is except that fighters should automatically scramble to defend if the city there in gets bombed
That or air superiority should be like fortify and stay active (maybe cost gold in upkeep or something over time)
Air vs Sea
First bombers should be able to sink ships, and they should get a big bonus chance to do so if the ship is at port (in a town). However, some ships (those equiped with anti-aircraft guns and missiles) should have a chance (maybe a very good one) to bring the bomber down. If the unit can't fire back it should be treated as bombardment but allow lethal, but if the unit can strike back it should basically be a normal combat or a bombardment with a dice roll for if the bomber is shot down. Possibly this effect should even include units within the area of effect, say a cruiser has a semi-air superiority role and can protect its fleet somewhat.
Air vs Land
It should work as it does now when the units are in a city. It makes sense parts of divisions of land units can hide in buildings or such and avoid total anhilation. Likewise units in a fort (gives them more of a purpose too) should receive similar protection from lethal bombing hits.
Units in the open should be able to killed or not based on terrain. Bombers should be most effecitve at eliminating entire divisions in deserts and the least in hills or forests.
Also some land units might should also have the ability to fire back at bombers, not sure. Maybe just a settable unit attribute "can attack air units" or something like that.