Quite. Using the same sophisticated method to judge whether there's demand for a service, 6 of the 20 Virgin services through Milton Keynes Central in the next hour stop there, an even more "tiny" 30%. These stops should therefore be removed, the impact of their withdrawl would be marginal.
Those services are not causing a problem, as MKC has enough platforms for them not to (indeed, Platform 6 was built to allow Platform 5 to be a bi-directional fast line loop). Deansgate is, as it does not; for it not to cause issues it would need 4 platforms like all the stations on the Castlefield line do, but only Oxford Road has (well, 5).
If they were causing a problem, there would indeed be a solid reason for their withdrawal. Watford Junction does not have a fast line loop, and there isn't really anywhere to put one without a full rebuild, and as a result it has been cut right back to 1tph of VT. (MKC platform 6 was easy to add as the land on which it and its feeder lines are located was completely unused).