Melchett, that may well have been the case but ever since I joined the fleet many moons ago there have always been plans to reorganise or rebadge. The Army put up a case to have them in the AAC in the late 80s for example. As you may recall, the Merlin was a political buy against the wishes of the MOD. A subsequent RAF review into cost savings in the SH fleet concluded that it would be cheaper to mothball the Merlins and with the savings on the through-life servicing costs buy and run another squadron of Chinooks...with the attendant increase in lift capacity! Interestingly there was a move to "marinise" the Chinook about 15 years ago so that it could be embarked. It involved a blade folding mechanism which required increasing the chord width to 49" IIRC!
From the above it's fair to conclude that the Navy have long been keen to have improved embarked helicopter capability and the the RAF has been ambivalent about the Merlin so it probably suited both services to operate one fleet each.