I don't know. It's true that other MMO companies have allowed time-cards from their games to be used with other games - that's pretty standard in the industry. So your question is a damn good one. It's possible.
But is this the case for Champions and STO? The other guy who posted in this thread...does have a point in being skeptical.
You'd need word from:
a) someone who's actually tried using a Champions time card on their STO account
b) a Cryptic rep.
I've not seen anything on the matter from either party.