Why wasn't Thomas acceptable?
Wasn't the difference that the Gnostic books contained the philosophy that man could work out his view o God without the church and the church couldn't have that?
To a large degree, yes. Gnostic nonrecognition of hierarchal authority was premised principally on the view that the resurrection was spiritual, not physical. The resurrected Christ could therefore be encountered and experienced by the laity, and was not an exclusive event experienced by the apostles.
By taking this view, the apostolic succession upon which the authority of the bishops, priests and deacons was based was undermined.