Strange, I can't replicate the bug with the Mughal Empire lord. Can you try downloading the 0.3 patch again and reapplying it? If there's a bug, please let me know.
As for divorcing your wife - I thought that happened often enough in real life that you'd have no need to do it in-game?
Seriously, though, I'm experimenting with some additional dialogues and functions for the wife character that no other NPC is capable of; basically I'm testing features that I also plan to incorporate in Hari Ragat, as testing those is a bit easier in this mod since all the new code is mine and I don't have to worry about conflicts with anyone else's script.
As of now your wife is effectively your diplomatic and financial adviser. The wife character is partly modeled on Queen Nur Jahan, wife of Jahangir. She was a powerful, even formidable woman who figured heavily in the political scene of the time, was said to be a dead shot, and would've made a deadly enemy. So what I'll do is create a divorce dialogue, but if you do so your wife will join the faction that hates you most
I'm also beefing up the perks gained from other character creation choices. If you chose rebellion, you'll start with a sizeable army; it'll be the easiest way to start the game. If you chose to abscond with the taxes, you'll start with quite a bit of gold. If you chose to disobey on a point of honor, you'll get a sizable relationship boost with the other factions.