I absolutely love Whirlwind - one of the best (if not the best) System 11 games - and think it's a keeper. However, you are in a unique situation. Given that the theme could be a painful reminder for your wife, I would replace it with something else. Hearing "The storm is coming" over and over can't be pleasant.
Pinball is supposed to be fun, a quick diversion from whatever else may be going on. If a particular table/theme/artwork takes away from that or evokes a bad memory, it defeats the whole purpose of having games to start with.
Either MM (I would probably go with MMr) or TAF is a great choice. Another to think about is Pat Lawlor's game from JJP next year, which should be a good match if you like Whirlwind but not the theme.