Just a few of my thoughts on this.
With city leaders, I'm sure if you looked into every Prince or Princess in the land currently holding thrones, you will find many discrepancies. On the other hand, you look at absolutely any other player in the land and you will find the same. People will play for themselves, you just have to decide how that will work out for you.
As for setting priorities....A person is not forced into a city, nor into an order. You pick the patron that's order most closely follows your own views, wants, and desires. You do the same for your city, and in turn your guild. So, in theory, none should clash with each other, as your views should not clash with your very own views.