Just a short answer here, as I don't have much time for a longer ones.
The strange deity conflicts are generally steeming from a particular event and less due to theological grounds. Could for example be so that to fight the evil of the world, either an old artifact of Toran had to be sacrificed or an old one from Prunilla. And if the party were of Toranites, doing the later would have been the likely outcome, although it afterwards created a huge gap between two otherwise good gods.
I did of course just made that story up now but I hope you do get the point...
As for a big clarficiation of what I consider, a good point of attack for hostile deity relationships, and this especially being true for evil/"bad" deities: You can be friendly, chatty, like any other close friend. But if it comes to the point that your "enemy" needs your help and your own god/goddess gains nothing from it, then you should avoid giving that aid and perhaps even try to push it towards an even bigger failure!