Hey there. Been reading the progress you've been making and I like the ideas you guys are coming up with. While I've never been a fan of werewolf roleplays, the down-to-earth perspective of this has piqued my curiosity. If we're still throwing ideas around, I had several concerning this military faction that the players would encounter.
Collecting werewolf bits for profit as a motive might work, but I think it would be more interesting if their motive was less "Arg, I hate things so I'm gonna kill them for money!" to more of an, "There are werewolves and something needs to be done." When I think of a military sect hunting werewolves, I see them more as a mop-up crew with things other military forces don't know how to fight.
Basically, they work for the government keeping abnormal things like werewolves, vampires, and other supernatural "undesirables" suppressed and making sure people keep thinking they're just a myth. If there are vampires living in the sewers, they send a strike team to exterminate them and then cover it up as a "police matter" or a " previously unknown terrorist threat". If werewolves are living in a town, they send some investigators before discreetly putting down the suspects and getting the local paper to call it a "series of bizarre crimes and murders" with "unknown perpetrators" to boot.
This gives the military a more three dimensional reason to exist. Now they're in it because they're trying to protect the general public, a good reason for going the lengths that they do to hunt paranormal anomalies. This change in motive makes them less faceless evil villains and turns them into a faction that has a good reason to come after the werewolves and it creates the idea that these soldiers aren't doing this because they're dicks and they're mean, but because they're men and women trying to do their jobs. It would even be interesting for someone to roleplay soldiers who are coming into the town once they arrive and see things from this perspective. They are human beings with their own emotions and perceptions after all.
It also makes this military force more of a danger. They're not untrained grunts who don't know they're gonna fight werewolves; they're explicitly trained to fight the unnatural and many of them have successfully done so before. They wouldn't need to send mobs and mobs of cannon fodder to get torn apart by the players, instead sending in a small team of specialists that will keep the players on their toes. These specialists are physically outmatched by stronger, faster beasts; so you can expect them to use tactics like setting traps, playing dirty, and use their superior equipment to their advantage. However, that's if the players want the fight to be more of a hunt rather than a mosh pit where we all type how many dudes that last punch just killed. (Let's be honest, fast paced combat in roleplays tends to become erratic.)
In the even that the specialists fail, the government can decide to go in guns blazing and just send in lots of troops from the same task force. That would be the big messy fight, but that's only if we decide we want that.
Finally, presenting the military in this light shows how the world deals with werewolves, and maybe even that we're not alone. It can also bring up that supernatural censorship and an end game choice can be whether or not the players want to show the world they exist and that there's a whole world of paranormal things out there. That's just slinging ideas around, but we can totally work in the consequences of what happens if the players win and want the world to know who they are.
These are just ideas I began to come up with while I read through this thread. I'd love to join and I'd also love to get a chance to play out this idea for a faction. I hope this helps and I hope this takes off!