I am pretty confident that a Mk13 would slot through the fight deck quite easily and that the Sea Slug system loading bay could be converted into a hanger with a new flight deck on the quarter deck.
Hmm, some things to think about:
1. The Seaslug magazine is not immediately below the flight deck: it's one deck lower and there's a level of "normal" compartments above it (mess decks IIRC), so anything you fit through the flight deck also goes through those. That's by no means impossible of course, since you could always re-arrange those compartments elsewhere, but it needs thinking about. A Mk.13 GMLS is two decks deep, so it would definately need some rearranging.
2. The Seaslug magazine is only one deck high whereas even the smallest helo hangars are two decks high, so you couldn't simply convert the former into the latter. Again, if you were redesigning the ship on the drawing board, you could re-arrange the compartments, but everything has to go somewhere and the two components, hangar and magazine, are not the same shape.
3. The quarter deck has very low freeboard: possibly too low for a flight deck. The step down to the quarter deck is two decks high, so you could perhaps have a stern flight deck one level lower than the real one, but not two, and in that case, the new hangar wouldn't fit under the existing flight deck level.
Suggestion: if you don't want too big a helo, what you could do is make a stern flight deck that's also an elevator. The hangar floor is level with the quarterdeck, the helo is rolled out backwards onto the flight deck, and the flight deck them elevates two decks to conduct flight ops. Is this a good idea? maybe, maybe not, but there are semi-precedents: the Tribal class frigates had an elevating hangar floor for their Wasps, several Soviet types had semi-sunken hangars where the helo rolled in (the hangar roof folded back) and the floor them dropped a deck before the roof was closed again, and the USN Virginias had a below-decks hangar at the stern with an elevator, although in that case the elevator was enclosed.
What would be interesting is if part of the space used for the sea slug magazine further forward could be used for Ikara and then Ikara launchers installed port and starboard in cut outs or behind doors in the hull sides in the midriff of the ship.
Certainly doable, since Ikara was way smaller than Seaslug, but only with the RAN Ikara system with it's horizontal magazine next to the launcher. The RN Seaslug had a totally different magazine arrangement, deep below the waterline like a gun magazine (of course the Leander installations
were converted gun magazines, but Bristol was built like that) with the missiles stowed vertically and lifted up to the assembly room on a hoist. The reason for this difference was that the RN wanted the option of using a nuclear depth bomb on Ikara, and felt that the Aussie magazine was too vulnerable, insecure (since it wasn't manned) and didn't allow the selection of two different missiles or for a nuclear bomb to be fitted and armed.
As it turned out, the RN never got it's nukes for Ikara, so in whiff world, you could say that they gave up on them earlier and bought the horizontal magazine system, and it's associated electric launcher rather than the over-complicated hydraulic one the RN actually bought, instead. I've certainly used the horizontal magazine in some of my RN ideas as it gives useful options for side-mounted launchers that don't use centreline space.
Another thought is replace the MK6 4.5" in A with a Mk42 5" and the one in B with a Mk6 3" twin or alternatively Sea Cat, BPDMS, Sea Chaparel or even a Mk22 GMLS for a double ended Tartar arrangement.
I think you could probably get a Mk.13 in B pos. Mk.22 was designed to literally drop into the same hole in the deck as a 5" gun mount, but Mk.13 is actually about the size of most below-decks gun houses, so if you're willing to cut a bigger hole in the deck, you can have a LOT more missiles.