Well, it matters as much as any regular season college basketball game does (which is to say, not much). It won't have any effect on how well either team does in the March crapshoot tournament. In terms of the conference race, though, it could loom quite large, particularly for MU. A loss really hurts any chance they have in the conference race, but a win puts them in a tie for the lead with KU having the more difficult schedule down the stretch.
KU and MU will play again eventually in the future, so I don't really view these last 2 games as the end of a rivalry or anything like that.