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I think reading it as praising God is the incorrect lazy interpretation, and you are correct in your initial reading of it -merely having the word hallelujah doesn't have to imply praise for a deity. It's totally about human sexuality and a man's relationship to a woman, though the context is informed by religion. There are references to forbidden knowledge (carnal), woman as temptress and and sinfuly testing one's faith, but also of an ideal that sexual union at its best and most perfect is also a religiously sanctioned and holy union (as the church indeed teaches). Classic Madonna/whore dynamic. The song is ultimately bitter though, because this is perfect union isn't realized. The man has been scorned, the perfect union is but a memory, and this leads even to a skepticism about God himself. I mean, the last stanza says it all.
So yeah. The ideal holy sexual/spiritual union is attempted, and ultimately not attained, and the man is left broken and stripped of his faith. Edit: the woman as temptress and cause of man's loss of his special relationship with god is referenced quite literally In the second verse. That is the biblical story of Samson and Delilah http://en.wikipedia.org/wiki/Delilah#Biblical_narrative what with the binding, and the cutting of his hair to remove his power and all