Yea, definitely seems like a bad deal to me. I would expect the selling price after Build Out Credit to be below $44k once you factor in the credit and loyalty. My guess is the dealer is already factoring this in to his selling price.
Also, unless you have questionable credit.. I would not accept a marked up money factor. That's crazy. In August I was presented a marked up money factor on a F30 and it was easy to convince them to drop the mark up.
I'd go back and tell them .00125 and $46k before incentives
Good luck.