Your other argument that runs shouldn't count unless they happen in wins is not a good one to me. If that were true, then the wins shouldn't count either unless they get you to a championship, and the championships shouldn't matter unless they get you in the hall of fame, and getting in the hall of fame shouldn't matter unless it gets you some skirt.....
But if you wanted to give the MVP out to the guy who scored and drove in the most runs in only wins, I think there would be worse ways to choose....