I don't really think the alpha became a swamp werewolf, what I think is that it was some other werewolf, since, when we were searching for a cure on the teacher's books there was a mention on how the werewolves weren't seen around Bareshade for like 30 or 50 years I don't remember exactly, and the herbalist themselve questions where did the alpha come from since, if, he was living in the area with the capability to create werewolves for so long then how come nobody noticed him, so I think the alpha split from some pack somewhere else and migrated to the forest near Bareshade and now another one of that pack is coming to the area or it was another type of werebeast(?) altogether or alternatively the white beast of the rumor could be the alpha fleeing from the area since he lost his position to Logan.
I think the chance of Ruben being involved in the swamp werewolf fiasco is very slim since he seems very interested in potion brewing and potion development and creating a variant of swamp creature doesn't really seem to align with that, and Hissh is kinda busy planning a coup so the only viable option for me is either the witch or something new is interfering with the swamp and is trying to strengthen the swamp creatures for some reason.
I actually think the golems are protecting a gem or something similar, since Ruben mentioned "the heart" or something it's been a while since I had that dialogue with him, that the father is protecting, I also don't think the father is even an emerine golem to begin with, and I'm not even sure why I think that, but in my mind it makes sense that he is another race entirely from the golems, and if I'm right then the plot with them could go something like the herbalist helping them develop some independence and learn to live for themselves contrary to living in function of another