No, I don't think that's correct. The formula is: préferer qqc à qqc.

This not a 'comparative' phrase between the 2 (houses) - it is an expression of preference by the subject of one 'to' (instead of) the other. 'Que' doesn't work in isolation in comparatives - a comparator such as plus, moins,  aussi etc is needed. In that sense, I think the statement 'Je préfère notre maison plus que la leur' may be acceptable grammar, but would be tautological.  Perhaps 'J'aime notre maison plus que la leur' would be both grammatically correct, and non-tautological. Would be good to get some further comments of clarification.