When class and background skills overlap, you can just pick whatever; 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, so it's uncertain as to whether this reasoning would still hold in this context. 

On one hand, even though this quote is in the context of backgrounds, the class and the Domain are still two different sources, and since this is all happening at level 1, you can just swap out the duplicate for any other skill.

On the other hand, as suggested by @Theik, "if you follow that line of reasoning, you can do weird stuff like pick perception from your class if you're an elf, and then because you now have perception from two different sources decide to pick any other skill, instead of being able to pick from any other skill from your class list. The backgrounds are flexible, the class skills are not."

However, since this is still during level 1 character creation, so just don't pick History from class, then there are no overlaps; otherwise this could potentially be a wasted skill (as you suspected, hence your "oops" in your question). Of course, as DM, you are free to rule either way, if you wish for this PC to have Perception...