I know that some theories are just here for the lulz, but just in case this one isn't, keep this in mind: Jenka is probably roughly two thousand years old, whereas Booster is probably in his seventies, eighties, or if he's taken really good care of his body, maybe even in his nineties or somewhere around one hundred if you really want to push it. Such an age difference just about completely rules out the possibility that a normal human and a witch are spouses.
While there have been speculations as to why Booster visits Jenka in the ending scene with her puppies if he lives, I think we can rest assured that there was nothing too serious going on between the two prior to that. If your theory were correct, Misery would have to be Booster's daughter, and Ballos would be Booster's brother-in-law. As for the messages in the Waterway Cabin, I do believe that those are written by Booster, but I think that the wife bore child message that appears if Curly dies is referring to Sue. But I guess that's the kind of thing that Pixel left up for the player to decide.