I think you generally stick with JT though I have a lot of questions about why Kevin Long can't get him going, and, indeed, may have made him worse. But tonight aside you still don't want him playing less frequently at the dish.
What would be interesting given how well Stubbs has hit in limited action is if they decided to go with a third catcher for a while instead of two infielders. But that won't happen, and Marchan probably wouldn't hit any better than JT.