Sorry about that x3 Maybe when I eventually get around to the remake, the player will be able to choose what to do about that particular dilemma.
SPOILERS
I kinda did enjoy killing them off though even though they were my favourite pairing in the game xD *Evil laughs* At one point, I wasn't even gonna have any sort of 'happy' ending at all, but then I figured that would be tooooo bleak, haha.