The main reason has to do with the two systems' fundamentally different ways of relating to exoteric spiritual systems. There is a phrase which I am sure originated with the Golden Dawn, but the only place I have re-discovered it so far is in Liber 30:
In the true religion there is no sect, therefore take heed that thou blaspheme not the name by which another knoweth his God; for if thou do this thing in Jupiter thou wilt blaspheme יהוה, and in Osiris יהשוה.That seems like a pretty tolerant, inclusive statement, doesn't it? Which is why I doubt it was original to Aleister Crowley; one of his suggestions for ringing in the new Aeon was to shout "ΑΠΟ ΠΑΝΤΟΣ ΚΑΚΟΔΑΙΜΟΝΟΣ" (Greek for "away, all evil spirits") at any servants of the "Osiran religion" that one happens to pass on the street - i.e., Christians. Even less pleasant is what Ra-Hoor-Khuit states in the third chapter of The Book of the Law:
(49) I am in a secret fourfold word, the blasphemy against all gods of men.This may come as a shock, but I don't have some kind of innate hatred of religions that aren't Thelema. Christianity in particular gets attacked quite a bit by "occultists", sometimes for good reasons (the Churches' aversion to Magic, for one), but usually due to what comes across as bitterness towards the more extreme, hateful forms of Protestantism common in the United States. I get it: plenty of Baptists, Methodists, etc. (but not all of them, by any means!) think all Occultists are Witches, who are therefore Satanists, and spread this kind of misinformation to further their political agendas.
(50) Curse them! Curse them! Curse them!
(51) With my Hawk’s head I peck at the eyes of Jesus as he hangs upon the cross.
(52) I flap my wings in the face of Mohammed & blind him.
(53) With my claws I tear out the flesh of the Indian and the Buddhist, Mongol and Din.
(54) Bahlasti! Ompehda! I spit on your crapulous creeds.
(55) Let Mary inviolate be torn upon wheels: for her sake let all chaste women be utterly despised among you! [emphases mine]
It's well documented that Crowley had his own reasons for disparaging Christianity any chance he got, and this undoubtedly colors his writing. I still maintain that the Prefatory Note to Book 4 is one of the finest essays on comparative religion I've ever read, and to his credit Crowley manages to confine his negative remarks about Christianity to valid criticisms of Church practices as they were in the early twentieth century. Unfortunately, his dislike is much more vehement in many of his other writings, and these - coupled with the fact that his pathological hatred of Christians seems to bleed over to an inordinate number of those calling themselves Thelemites - are part of why I cannot earnestly call myself a Thelemite.
(I have other problems with The Book of the Law; while I think the first chapter is full of beautiful imagery and a positive spiritual/moral message, the second is less so, and the third least of all. I have a great deal of respect for Christianity - Catholicism in particular - and so I can't call myself a Thelemite in good conscience.)
Going with the linked authors' computer metaphor, Thelema is only kind of Golden Dawn 2.0. Imagine the Golden Dawn (Outer and Inner Order) system as a set of incredibly useful, versatile programs. Then, someone comes along and sees that the framework and a few of the programs are good, but their own vision for "computing" is different; consequently, they re-write much of it so that it's more customizable and free-form, while also building in some of their own ideas.
[EDIT 2015-05-04: Fixed the OSOGD link.]