I would let them work it out. Watch them, of course, if you have time, but let them deal with it. I agree with you that it's probably a pecking order thing.
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He would approach her in attack mode, puffed up and aggressive. She would react and stand her ground and the fight was on! He didn't even get more than a few feathers out of her before I intervened. Normally I would stand back and watch, letting them figure it out themselves, but he is a larger rooster around 8 lbs (calling him that as he has begun doing the rooster jobs, I do understand he isn't technically a rooster yet) and she is on the smaller side around 5. I didn't want him to severely hurt her and have more chicks to raise indoors as well as an injured chick.