How to reconcile one single morality with a polytheistic religion:
1: Every god has the same morality, there are no moral differences between the gods. The differences are in terms of whether a god is of lightning, wind, death, crops, rain, etc.
2: There is one 'god of morality', and that is the god whose morality must be followed. The other gods are not moral-givers, though they may be useful to have in a pantheon for other reasons.
3: No god by itself has the full morality, the one morality is constructed from the prohibitions and requirements of every god added together. Either this cause no contradiction, or, if a contradiction arises, then:
3.1: Whenever there is a contradiction about the morality of a specific action, then that action is deemed allowed.
3.2: Whenever there is a contradiction about the morality of a specific action, then that action is deemed prohibited.
3.3: One of the gods is either ignored (in terms of morality) or kicked out of the pantheon. There may be methods to decide which god's morality to reject.
4: Rule of the majority of the gods (opinions of equal worth).
5: Rule of the majority of the gods (opinions' worth may differ, for example based on the deity's strength or wisdom).
6: Rule of the majority of the strong gods.
7: Rule of the majority of the wise gods.
8: Morality has nothing to do with the gods, but there is one, say, "objective" morality, based on "society's best interest".