On a side note, I was disappointed to find out that the poly relationship isn't the protagonist, Wyll and Karlach.

Hell yeah, pun intended. But really, it would have made a lot of sense. It would have made a lot of sense that not killing Karlach saved Wyll (because of the breach of contract and her testifying) and that Wyll saved Karlach because he could help her fix the informal heart. Also, way hotter than Maryzora.
Now, more serious. I like many of the ideas that would tie Wyll with Baldurs Gate politics. IT would make a lot of sense that Maryzora was trying to manipulate the politics by trapping Wyll. And if Gortash was involved in that, then it makes even more sense. After all, Gortash sold Karlach to Zarial, who is to say that didn't make another deal where he wanted Maryzora to seduce Wyll, and then use that to undermine his father and take his place in the council. That could force his father to throw Wyll out of the guard and the city, which was part of the original story. So not that difficult to tie in. And as people said, if he was a noble and a hero in Baldurs, then he should have friends.
As for adding Maryzora to his plot, it would make more sense that Maryzora worked for Gortash because they have deals together. So in Act 3, if you want Wyll to remain in your party and keep working for you, you need either to make a deal with Maryzora or beat her at her own game by proving he broke the deal by asking to hunt Karlach. Anyway, right now seems unlikely.