And none specifically say anyone would become god or immortal if they understand the mystery, did they?
If I'm understanding you, I think the argument you're making is that the wording of the Gospel of Thomas would have been too closely associated with very specifically gnostic ideas about metaphysics, and about the nature of salvation and "knowledge", in order to be made orthodox. I think it's a valid point, but I guess what I'm saying is that this is something of a matter of interpretation, and it's not clear to me at all that the text, in and of itself, is impossible to read in a less explicitly "gnostic" way.
Outside of the context of establishing the canon of the N.T., I think the writings of Pseudo-Dionysius are a pretty good example of the idea I'm getting at. They are obviously heavily influenced by Neo-platonism, and it's not a great stretch to interpret parts of Pseudo-Dionysius in an explicitly Neoplatonic way that would have been at odds with Christian orthodoxy. Instead, his writings were interpreted into orthodoxy, as they were read and expounded upon by Maximus Confessor, John Scythopolis and other more orthodox sources who valued them and filed down the Neoplatonic edges, so to speak.
In a similar way, if we begin by assuming that the text of the Gospel of Thomas must be read with the gnostic understanding explicitly presupposed, then it's clear that you are right that it would be excluded on those grounds. But I think an appreciation of the history of interpretation of texts makes clear that it is by no means necessary, either logically or historically, to make those presuppositions. An enterprising orthodox theologian could quite easily give a different gloss to the text, and render "understanding the mystery" in an orthodox, and not gnostic, way. It would not be
that different from a reading of 2 Peter 1:3-4, in which becoming "partakers of the divine nature" depends on promises granted "through the knowledge of Him who called to us."
Now, clearly it's no more necessary to interpret the Gospel of Thomas in a more orthodox way than it is to interpret it as explicitly gnostic, but my point was only that it didn't seem clear to me that it was literally impossible for Thomas to be given an orthodox gloss. As you yourself said, 1/2 of it is already in the canonical texts...