Once again, as far as we can tell, units don't get killed from single actions in Civ5.
Heck, in Civ4, a fully healed airplane unit isn't shot down in a single action either.
In effect, you want more granularity. But more granularity means longer turns. And they are trying to cut down on the granularity of Civ unit management, especially in the modern era.
If an intercepted fighter loses a bounded amount of HP from a failed mission (against a given set of defences), and can act more than once per turn, then a single fighter can emulate to a high degree of accuracy the "there are 4 fighter units on a carrier", except you don't get 4 distinct units.
Given that you can emulate the behaviour of 4 units (with some obvious exceptions -- you cannot split the fighter into 4 units and send them to 4 different cities, or have 4 understaffed carriers, etc) with 1 fighter unit, what concerns remain?
Because, you can do that emulation. And it is already being done in previous versions of Civ, where a N fighters on a carrier doesn't represent N individual fighters.
Ah, so the fighter "unit" on a carrier would have four life bars and four action points (corresponding to four missions) and when one of these life bars is empty, it loses one action point? It's a Rube Goldberg machine of a unit.
How exactly does this cut down on the length of turns? You still have to order it to perform all four missions. Does that really save any time over ordering four separate units to perform one mission each? I don't think so, since Civ automatically jumps to the next unit when the current one has finished its move anyway.
Edit: Another thing you neglected to mention is the ability to hold units in reserve and shelter damaged ones. With four units on the carrier you can shelter three damaged ones and still carry out missions with the last one, something impossible with a single unit.