The choice of making her Divine really is something of a double-edged sword. On the one hand, you're making sure the mess that occurred between the templars and mages never repeats itself. On the other hand, you're putting Leliana in a position that has the potential to fundamentally change her as a woman, thus possibly affecting any current relationship with the Warden in more ways than one.
To me, it sounds as though there is no correct answer, only a logical answer. What you deem logical depends on one's priorities. As in, is it the relationship you're worried about or is it the war? Is this more of a personal or a political decision to you?
It's something that I think the writers even intended, having to choose between two paths with no real idea as to the consequences associated with each.
I think the conflict between Mages and Templar is already solved regardless of who your Divine is by the ending of Inquisition. Of course some people might argue one Divine's decisions and teachings are better than another, but considering how the narrative being unfolded in the past three games so far, I doubt Bioware would drag the Mage-Templar conflict to the fourth game - unless it is something necessary and planned beforehand.
I agree though. Divine rules over half of a continent and whoever sits on the Sunburst Throne would change the political situation in Southern Thedas significantly. In the case of Leliana, her relationship with the Warden would become really complicated for sure, especially if we're overanalyzing it and think that our Warden's origin would affect the relationship in one way or another.
That's the best part about making decisions in Bioware games in general. You are given these narrative puzzle and you can set them accordingly to your likings. Some decisions might look good or bad at the outset, but events of future games might force us to change our decision in the Keep e.g. Alistair is staying as a Grey Warden, Morrigan's Dark Ritual among other things.