Probably not an accident that the last was Greek. It's true that Greek polytheist paganism was -- hmm, I defined it as the first type here (you may want to read that) which, being not a separate thing from life in general, tend to be highly syncretist. But Greeks also came up with philosophy, which tends to be absolutizing. If you read Maccabees, and compare it to early complaints about other pagan conquerors, you will notice an enormous difference: the Hellenizing forces were out to change the religion practiced.
The earlier forms of religion practice might have conflicts too. Introducing new gods, as was claimed of Socrates, was probably less of a problem that impious behavior towards the acknowledged gods. Roman legions had their rota of sacrifices that must be made -- including a slew of different titles attached to Ceres -- but there was no suggestion that you couldn't worship other gods. Or performing rites incorrectly. Julius Caesar, pontifex maximus though he was, properly did not attend the rites of Bona Dea, but he divorced his wife, who had presided, for the scandal of a man intruding on them. Offending a god would have serious consequences, as would ignoring some ritual impurity. As at the opening of the Iliad, the first question of any serious catastrophe would be whether someone had ticked off the gods. And it's not an accident that word "magic" comes from magi, the Persian word for priests; not to mention that magic itself could be prosecuted for impiety, one could also regard weird religious practices as not really religious.
But it's with the rise of philosophy, and the second type of religion, the type that knows itself by contrast with the first type, that religion really gets it potential for conflict revving up. That's when people start to argue about whether the views are right or wrong, and what sorts of worship are excluded. Lots of potential for stories. Modern day tolerance would be regarded as insane during most of them, because the potential of annoyed gods making life difficult would not be underestimated.
Except in fantasy fiction, where a lot of time worshipping whatever gods happen to strike your fancy is a hobby of yours that has no social repercussions, and objecting to this notion is a sign that you are Evil. This is improbable.
And when writers introduce religious conflict, they frequently steal a real world exemplar -- not a bad idea -- and in the process of filling off the serial numbers, file off the numbers that happened to explain why people fought over something. It's really hard to have a theological dispute when you neglect to provide either side with any actual theology to argue over. It's hard to have the conquerors persecuting the religion of the conquered without some reason, either theological, or objecting to the form of the rituals (such as human sacrifice); contempt is another matter, but if they object to their religious practices, there is probably a religious reason behind it.