As with when class and background skills overlap, you can just pick whatever, so letting them get Perception is fine.
From the PHB, pg. 126:
If a character would gain the same proficiency from two different sources, he or she can choose a different proficiency of the same kind (skill or tool) instead.
This quote is in the context of backgrounds, but the class and the Domain are still two different sources, and since this is all happening at level 1, just swap out the duplicate for any other skill.
At the very least, since this is still during level 1 character creation, just don't pick History from class.