Not sure they are being blocked, but in the morning thats exactly what Virgin would want to happen, they dont want shed loads piling on at MK and using it as a commuter service.
Must have been a change in policy then as Virgin used to run a commuter service from Rugby via Northampton and MKC.
Used it several times when it was the last 87 hauled diagram as it was a short detour off the overnight Holyhead boat train connection.
It was very lightly used from Rugby, the preceeding Wolverhampton taking most of the passengers but had a very heavy loading at Northampton and seemed full+standing in standard from MK.
I agree that staff would be correct in stopping someone boarding a set-down only service or even removing them before the train left the station but I cannot see how an ALR holder could be charged anything or fined if they were able to board and remain on once the train had resumed it's journey. I find it very unlikely any court would uphold a fine on that basis.
I must say I was tempted to bail out at Wolverhampton on a W&S service earlier this year on my Britrail pass just to see what reaction it would provoke from the Virgin staff but as I was going to Shrewsbury and did not fancy an hour on an ATW 158 I stayed on.