If you had to draw a line between "pagan-themed" and "non-pagan themed" decks, I would put Thoth definitely in the "pagan-themed" category.
First, it comes from Crowley. He wanted to "restore paganism in a purer form". I'm quoting from memory - I believe he said this was his mission, remembered from a previous life when he met with a council of illuminates who vowed to reincarnate with various missions.
Secondly, we have to remember that in Crowley's time, there was no organized neo-paganism. Paganism was something you read about, and tried to live if you wanted. The main thing for wannabe neo-pagans was to find the essence of the pagan philosophy, gleaned from syncretic accounts like Frazer's in "The Golden Bough".
Third, Thelema (as Aeon appropriately points out) is not Paganism; Thelema is a word which sums up a philosophy. In Liber Aleph (IIRC) he compares it to the Christian Agape (Love) - or is that "INRI"? - , the Buddha's "Anatta" (No soul), and four others (7 words of seven great prophets). You could find out surely just by typing a few key words in Google. In this way, Thelema is to paganism what Plotinus's Theurgy was to paganism - a philosophy within a framework, which used the symbols of the framework to gain true Self-and-transcendental knowledge. Anyway, I think Crowley would have said (and probably did somewhere) that paganism was more conducive to the aims of Thelema than any of the dogmatic religions.
Last, I have the strong impression that Crowley saw himself as a pagan. If you read "The World's Tragedy", it is a passionate plea for the revival of a pagan way of life - which he understood as seeing life as a dance of joy and pleasure, however hard sometimes, rather than as a "veil of tears", which is how Christianity normally sees it. I believe that Crowley really wanted to convey this sense of life to the world, a pagan way of life as he saw it, even more than he wanted to convey and teach the difficult art of Magick and the Knowledge and Conversation of the Holy Guardian Angel.
It is my belief that Crowley enjoyed life in this way, and that the reason he always had friends was because he lived it this way (this is the reason he had enemies too).