As for monotheistic religions working better together than churches of different gods of the same pantheon . . . well the real world should disprove that better than I ever can
Even two different sects within the same monotheistic religion can be violently opposed to one another. The problem, IMO, from the versimilitude perspective is that you would think a deity and his servants could pretty easily put an end to theological debates about the will of the deity.
For example - succession (ie. who's going to be in charge) has been a cause of schism in real world religions. But it's hard to imagine such a thing happening in a world where visiting angels and commune spells and such exist. Yes, you can imagine some local fraud/deception with regards to this, but it's hard for me to imagine a thousand-year division among a gods worshippers not being settled by the deity himself.
And this relates to my overall feelings about monotheism in DnD. First, I'm not sure what kind of monotheism we're talking about. Perhaps the "you should have no *other* gods before me" sort of thing - a tacit recognition of the plainly (?) demonstrable fact that these other gods exist. So really, monotheism is just a taboo of sorts placed on the followers of a certain god that they never pray to another god. Doesn't seem to much different than a typical DnD campaign.
I think a "no other gods exist" type of monotheism would be a lot harder - given how close the outer planes, and divine servants, and clerical magic, etc. are to the world's inhabitants. If other gods don't exist then where are there clerics getting their spells from and how long could that go on before (with the help of divination or trips to the astral sea) the whole thing were detected? Or the other gods do exist, and the mono-god is lying about it - which has implications on alignment issues. Or maybe you can venture into some equivication, for example some sort of pantheism where the other gods are aspect of a universal god. In fact, given the seeming complexity of real world religious explanations for things (ex. the trinity) maybe I'm being too picky.