I find it interesting that the reviewer thought that the Hammerites are "poking fun" and "Christians". I would say, rather, that the Hammerites are specifically a reference to the darkest aspects of, very specifically, the Catholic church during the Middle Ages. They are clearly portrayed as hardened fanatics who use the strength of ascetic dogmatism, political machinations, and physical violence to spread their Word, all the while obsessed with building giant and claustrophobically dark cathedrals. This is more prevalent in the first two games, actually; in the third games the Hammers are much more toned down, to the point where it seems perfectly believable that that might be a real religion in our world (if it wasn't believable before). You also mention the Pagans as being portrayed in a better light that the Hammers, but this is I think due to your own sensitivity on the issue. In the first Thief game, the pagans were the main enemies and were portrayed in in a very dark light; there were, in fact, no human pagans. They were all twisted humanoid monsters or wild animals, a deranged cult that had as much to do with violent torture as it did with nature. The end of the game has you killing (or at least debilitating) the god of the forest. The second game of the series focused on a "protestant" faction of the Hammerites that had broken away from the main doctrine, and who was devouring the world with machinery to the detriment of all life.

This game, the third in the series, was meant to thematically balance the first two while Garret attempts to find balance in his own life. So, you have the choice to either befriend the Hammerites or the Pagans–or both–as much as you want. The Hammers are in fact barely present in this game compared to the previous iterations, and their presence here is almost solely devoted to standing around in their churches and chatting. In terms of being offended by their presentation, it seems like what's bothered you might be the mere portrayal at all of a Christian-like group that is not actually Christian. Also, it's a hammer. It is shaped exactly like the hammers the Hammerites actually carry. It's a sledgehammer; sledgehammers are symmetrical. Which is not to say that the allusion to the cross is not entirely intentional.

However, none of the factions in the game world was meant to satirize or to literally represent real-life groups of people. They took the tone and methods of some historical groups that had an interesting seed, and wove them into the story to create something original. Every time I play one of the first two Thief games I realize I have forgotten how interesting and intelligent the quotes are, supposedly coming from the books and scrolls of the Hammerites, Keepers, and Pagans. They are certainly not just plundered from the Bible, but are in fact quite original. They each represent a very different view of the world, and none of them are entirely evil or wrong. The whole point is that you, Garret, stand as a neutral entity outside of all these warring ideologies, enjoying the freedom that is possible in a life without rules. It's not advocating anything, not even Garret; it's just a very interesting world.