That's an very good point Kilak, and one that isn't brought up enough.
On that same note, since it is polytheistic there is no real first commandment edicts for /most/ deities. A priest of Sune would have no problem praying to Umberlee (evil or not, she's the one that will sink ya if you don't) for a safe voyage on a long trip - it's just the way it works in polytheism, it is why many cities in Faerun allow "evil" temples within their walls. Praying to a god does not equate revering a god. And praying to Loviatar before a birth, begging to lessen the pain of labor, isn't a bad idea in the slightest...but maybe you should save the bedside shrine for Helm
And as far as opposing religions go, it's tough. It'd probably be different from religion to religion. Most evil religions, ironically, tend to be more willing to converse...because, to quote Animal House "We need the dues!", and a silver tongue can do that better than just killing them. Good religions, knowing this, likely avoid conversations with their opposing faithful for that very reason. But if the good pc knew the evil pc beforehand, I think a civil conversation could be had, without a doubt.
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Also, as in many polytheistic pantheons, if you travel to a different "land" you'd likely feel better off praying to that lands gods along with your primary. Right now, with the areas that are coded, it wouldn't come up that often. But if you somehow found yourself in the Underdark, you'd probably feel more immediate connections to the gnomish or drow pantheon, than what is commonly held on the surface.
You can honor even the gods you hate the most, your religion isn't one deity, your religion is a pantheon of deities...and sometimes even more than one pantheon! But, obviously, if you choose to dedicate yourself to a small aspect of your religion - much like worshippers of a specific saint in catholicism - you may be forced to deal with certain followers of other deities in a presuggestive way. Only research into your PC's god will tell you what is appropriate - but in general most everyone can exist without screaming at eachother.