If Thompson wants to play and can play, he absolutely should. Wherever Howard may end up, Thompson is lightyears ahead of Will Howard right now, and, right now, we're sitting at the top of the standings. We can do some really nice things this year. Putting together something like a 6-4; 7-3 type season would be GREAT for the program (and obviously anything better would be that much better). Turtling and "playing for the future" by starting a freshman would be stupid, given how much better Skylar has been so far this year, in a season that's still very much "in play" for goodness/greatness.
Plus, I don't think it's always true that starting a true freshman QB is good for that QBs long term development. I think there's a lot of value to be had for Howard to get in there, learn the offense (generally) and bend bars, rather than "taking his lumps."
Howard has a bright future regardless of whether he starts the rest of the season.