One as someone interested in the early church, I must disagree with some of your points and present you a few arguments in response,
One the majority of evidence linking the Gospel of Thomas to Gnosticism is based upon the fact it was discovered in nag hammadi with gnostic works , however within nag hammadi there were also found platos republic.
From your own arguments against it
1) its dependence on more than half of the New Testament writings
How exactly is that a bad thing? The Gospel of Luke is clearly based upon the writings of the apostles and
disciples that preceded him.
2) its likely mid to late second century Syrian influence,
Can you please elaborate on that, after all we were first called Christians in antioch, which is in Syria in the 1st century A.D. and what influence is there between 1st century and 2nd century syrian influences? as in how does one distinguish the two?
3) its heretical nature with Gnostic overtones,
such as? Granted the Gnostics are from without, and not part of a Christian tradition, however the fact that the G.o.T. (Gospel of Thomas) speaks of mystery and knowledge this by itself is not enough to declare it a Gnostic work after all there is the very serious matter of
The disciples came to him and asked, “Why do you speak to the people in parables?” 11 He replied, “Because the knowledge of the secrets of the kingdom of heaven has been given to you, but not to them. 12 Whoever has will be given more, and they will have an abundance. Whoever does not have, even what they have will be taken from them. 13 This is why I speak to them in parables: “Though seeing, they do not see; though hearing, they do not hear or understand. (Matthew 13:10-13)
4) its lack of references from early church fathers or first century witnesses,
Origen used it though he did not declare it Canonical,It is infact very likely that the G.o.T. may have been touched by Gnostic writers but the fact that he used quotes directly from it
"Whoever is near me is near the fire. And whoever is far from me is far from the kingdom.”
Origens use of this and other sayings from thomas implies he believed in the authenticity of those particular sayings as though Christ himself had indeed said them!
This same saying is also used as authentic by Didymus the blind.
5) its disagreements and variations from the first century context of the New Testament gospels,
Such as?
6) its self-conscious promotion as an apostolic book which reflects a later time period. In fact, even many adherents to a first century origin for the Gospel of Thomas argue that, in its present form, Thomas reflects later editing.
Well again from Origen we do learn that Thomas was part of the 12 and was often writing what Christ said, Both Origen and Jerome talk about a sayings gospel it is possible that there was a better variant of thomas which was untouched by gnosticism when you actually study the early church and the patrist fathers of this church, you will come across something called the Agrapha which in many ways touch on Thomas and co-incide with it.
The gospel of Thomas does not in any way share anything to do with the Real Jesus of the Bible
again based on what evidence? there are sayings in Thomas which coincide with the synoptic Gospels and even more which coincide with the agrapha.