I thought that having it be a religion could be nice, but actually upon further reflection, it's not so great. That's because once again we reach the same point as was mentioned by archaeo in one of the threads linked earlier:
We've tried to come up with a werewolf species a few times before.
The problem as I see it is that Crawl already has a "become more monstrously powerful with XL species" in Demonspawn, and it already has "transform into a dangerous beast" with Transmuters. In order to make a Werewolf species different, you end up having to pile on a ton of complicated, fiddly mechanics, only to end up with something that does what DSTm does with twice as many moving parts. Crawl already has too many species that are just near-copies of other species.
viewtopic.php?f=8&t=18116&p=248254&hilit=werewolf#p248211
Basically, whatever powers that a werewolf species or god would give would be in conflict with other things that exist in the game, and thus be redundant, regardless of the method of transmission.
That being said, I think we already have a lycanthropy mechanic in the game, it just goes by a different name:
berserkitis. All you would need to do is remove it from the list of mutations, turn it into a "curse" that can only be acquired by being bitten by some sort of werewolf unique monster (that appears in maybe 1/3rd of games, around D6-D8), and add some minor buffs to the actual mutation to make it situationally useful.
The curse mechanic could be a series of messages like "You feel slightly/severely/irreversibly cursed with the full moon's madness" which would apply a "CURSED" debuff of a whole new colour, and basically be cancelled by reading a scroll of remove curse before reaching "irreversibly".
In terms of what the curse would actually do, it would just be a modified version of berserkitis. This is what berserkitis does right now:
1 1% chance of berserking each time you attack. Reduces chance of passing out afterwards to 3%.
2 Same, with a 3% chance of berserking and 2% chance of passing out.
3 Same, with a 9% chance of berserking and 1.5% chance of passing out.
Lycanthropy could just add a progression of +fighting skills or apt, claws, and/or random appearance wolf allies that then attack you at the end of your transformation. Maybe this berserk would leave you exhausted but not slowed? I am not exactly sure about what would make this unique/fun, but I think it should offer something more than simply just berserkitis, otherwise it would just be stupid to ever *not* uncurse yourself.
As a final point, this mechanic could be used for other curses, basically turning curses into a new type of mutation that is permanent once it "sets in", and comes with severe downsides in exchange for potentially cool character options.