OK, I'm on the fence about this then. If you HAD to go to either an Empire system or Shinrarta to buy an Empire ship then I would say of course you shouldn't be able to buy them from Del Boy Trotter's Fleet Carrier. But if you can get them elsewhere then it becomes less clear cut.
I think in practical terms you can divide the galaxy into three bits for this question:
1) The bubble (including Pleiades, Witch Head, and outlying systems)
2) Deep space
3) Colonia
In the bubble, you're never more than a few minutes from a system where you can buy a superpower-aligned ship (including things like the Chieftain or T-10 or Imp Eagle which aren't rank-locked but are superpower-locked), so it doesn't really make much difference if a carrier is selling them too.
In deep space, you can't normally buy the independent ships either, so if a carrier can sell those it's hard to see why it shouldn't also sell superpower ships. You still have to get the carrier out there, with the ships taking up hold space and reducing jump range, and then you have to take the carrier back once it's done to pick up more stock.
Colonia is probably the one place it gets interesting - you can normally buy independent ships, and a certain Anarchy faction sells some but not all of the superpower-aligned ships conditionally on it holding control of a certain station. So being able to sell superpower-aligned ships from a carrier would make a significant difference there, since there's a carrier shop out here.
The compromise which preserves the distinctions between those places is probably to allow carriers to stock superpower-aligned ships, but to only allow them to buy the ship packs when in a system controlled by the relevant superpower. No extra problem in the bubble or deep space, but if you want to set up a Cutter shop in Colonia, you'll have to make regular trips back to the bubble to buy more Cutters.