If the intercity service was ever merged with the types of service Virgin would not want to have anything to do with, could Stagecoach bid (as per the ECML) and then use Virgin to brand only the Intercity trains, and its own (or another) brand for the rest?
Would a franchise allow such a thing? It would still be one operator, but the masses would still think Virgin was running only one service.
There is a precedent for this!
I give you Gatwick Expeess being operated by Southern!