I believe they wanted to change her stern. The magrodome took up quite a bit of deck space, and with the Alpha and Beta tenders there, I've heard that the passenger flow and deck space in that area wasn't great. Also, the space that the pool took up was replaced by the Pavillion galley.
It was never about Cunard wanting to change her stern, it was though about changing tastes in cruising with guests wanting more relaxed dining options during the day. The QE2 as originally designed had two open air swimming pools ostensibly for when the ship operated as a two class vessel. The Magrodome was installed in '83 in an attempt to establish an area for buffet style breakfast and lunches resulting in a triple purpose space: a buffet area, an indoor lido pool and an enlarged night club space. This created more problems than it solved: firstly the space set aside for the buffet servery on the port and starboard sides coming through from the Queens Room was inadequate, secondly the pool itself was under-utilised for those in swimwear were not comfortable using the pool alongside guests taking lunch, thirdly the roof space created a "well deck" space immediately outside the old Yacht Club which was used for sports but ruined the step down appearance of the aft decks and finally, the problems already mentioned regarding opening/closing the roof. More often than not the pool was not filled with water, particularly on the TA so became somewhat of a redundant space.
This situation remained for 11 years until '94, when it was decided to remove the pool entirely, enabling an upgraded buffet area to be installed on Quarter Deck, with better seating. The supportive box the pool sat in could be removed on one deck enabling an enhanced servery/seating/galley area for those on the open deck in sun/swimwear wanting lite meal options. The space above the Lido becoming an enlarged Yacht Club as the night club and an improvement in the open decks just above.
You are right though Adam that with the installation of the Magrodome there was a quite cumbersome route down from the open decks on Sports and Boat Deck to Upper Deck outside the Yacht Club, back up to walk along side decks over the Magrodome and under Alpha/Beta and finally down two flights of stairs to the One Deck Lido. Those '94 changes gave back to the ship a more attractive stepped down appearance to the aft decks and increased the area of available open deck space.