You're quite right, the M2 aircraft was a floatplane and was recovered after landing by crane
But it was launched off the foredeck by catapult
It was a tiny aircraft - the Parnall Peto and maybe couldn't get off the water with pilot and observer on board.
There was an excellent article on it in "Aeroplane Monthly" a few years back.
Pity they forgot to close the hangar door when the submarine dived though.