The main problem would be the bomber type fighters. They have the same problem as missile spam. That they can achieve a critical mass. As it is now, a pair of Drovers, if they can Strike/Eliminate if they happen to be working together will destroy cruisers in a couple of passes and move on to the next cruiser. I don't really like the "new" system as the player feels helpless and out of control and sometimes the amount of fighters assigned feels completely random. Then again, the lack of control in a battle is as designed and is not unique to carriers in particular.
It'll be difficult to retain the feel of bombers and balance it whilst giving player agency.
Its true that 2 Drovers can take on a cruiser in a few passes - but is this different from 2 normal high performance destroyers? After all, Drovers are 12 deployment points/supplies, so 2 of them is nearly the same cost as a cruiser (and you can get 3 Hammerheads for 2 Drovers, or 3 Enforcers for just a bit more). And if the cruiser is actually fitted for anti-fighter, or is part of a fleet fitted for anti-fighter, it will be almost completely immune.
Fighters are simply better missiles than missiles.
Astral with six Perdition wings and a carrier officer will destroy big things quickly and efficiently.
The advantage of missiles that they will sit there and be fired on demand by a ship mounting them (and the ship is generating opportunities), while fighters are limited to doing runs and getting shot down. Fighters are certainly powerful, but not completely missile replacements.
Re: Astral. It is indeed a powerful ship, and Perditions are powerful fighters! I would say Astrals are about right for a Capital ship, being no more powerful overall than an Onslaught or a Paragon, but they can be specialized for anti station/capital work quite nicely.