Many couples experience this apparent conflict. Remember you have many choices:
The four "good" sectors and the four "bad" sectors can each be strong or weak depending on what direction they fall in... so a house with a sitting direction suitable for you may not be so bad for her.
If the house sitting favors one partner, the bedroom sector might favor the other.(and yet not be hard on the first resident)
If the House sitting favors one partner, the bed direction might favor the other (and yet not be hard on the first resident)
If the house sitting favors one partner, the main door location might favor the other.
But all of this is secondary to selecting a well proportioned house in a good setting with suitable external forms and internal qi flow. If these things are good, they will outweigh the potential drawbacks of the house kua. And if these things are bad, the potential benefits of the house kua will never materialize.
Once you find such a house, and if the sitting is auspicious and useful, the main door is auspicious and useful, then make sure that the location of the bedroom (and, if someone works from home then their office as well) is auspicious and useful. This will put you on a good path.
And, of course, there are other feng shui methods to look at to make a wise choice of a house.
Good luck!