does JT give them the best chance to win now?

probably but...

is JT the long term solution at qb?

no. actually at this point most likely none of them are.

do the 49ers know enough about Alex Smith at this point to know for sure that he isn't worth the time?

I don't think that is true. which is why they need to give him another shot this year. don't want to go thru this again next season with him.

maybe Nolan thinks JT is better short term and is worrying about his job