Legally, it doesn't matter whether or not Virgin are losing out. The tickets are not valid without a Railcard, and the Railcard is not valid if there are not two passengers travelling together.
The train companies in this country doesn't really care much for common sense or providing good customer service. Those are the rules and your only option is to rebook if you want to be legally in the clear.
Of course, you could hope that the train manager is reasonable and accepts you travelling alone if you produce both tickets and the Railcard, or that you are able to find a ticket office that will excess away the Railcard restriction (very unlikely!). But if you cannot do this then the only alternative is to risk being charged an additional fare.
I think this is one area (out of many) which the TOCs should take a long, hard look at when they ask themselves why the rail network has a rubbish reputation. It's ludicrous not to have a policy of simply letting you travel, as long as you produce both tickets, but that is the way it is.
