Shouldn’t Baelor had of effectively abdicated himself in having the High Septon dissolve his marriage to Daena AND become a septon himself? Let’s say Viserys is a different man – how il/legal would it be for him to depose his nephew in a bloodless coup (just let Baelor do his thing without kingly power), especially considering Baelor’s antics in Dorne and his extremism (like imprisoning his sisters on top of aforementioned) upon returning to KL?

That’s a good question. You’d think if Baelor was such a holy man who wanted nothing to do with the secular world, he would have abdicated in favor of one of his relatives. Indeed, the fact that he refused to conssumate his marriage a year before he was crowned would suggest that he was already going in that direction.

However, when Baelor takes the throne in 161, his immediate goal is peace with Dorne and in order to accomplish that, he has to be king. So at least during his treck through Dorne, he accepted that his royal status was a necessary evil. Then he goes into the snake pit and things go a little out of control.

After he wakes up from his coma, Baelor is pretty firmly of the belief that the monarchy now exists to push his spiritual agenda – starting with the dissolution of his marriage and taking septon’s vows, then imprisoning his sisters, then banishing sex workers from King’s Landing, then building the Sept which he saw in a vision. As WOIAF says, “the king’s edicts were becoming more concerned with spiritual matters at the expense of the material.”