I think moulting onset is determined by date of birth, genetics, health etc., i.e. a sick chook can go into a random moult, so can a very stressed one, and a chook hatched a the non-usual time of year will moult at a possibly inappropriate time. But maybe the other hens or the rooster are helping her moult? Or maybe she's sick or has a problem of some sort the rooster can perceive and that could be why he attacked her. There could be so many reasons... I've never seen a rooster object to a hen being dominant to other hens. I have got one now that's dumb enough to make every squabble a random free-for-all threesome. Not my breeding there.
As for reintroducing her, and getting her to be less dominant, I don't know. You could try separate watering/feeding/perching areas, even if they're near eachother, just to give the others a chance to move away and keep eating/drinking/roosting. She'd have to chase them, not remain lording it over one spot. I give my chooks multiple feed and perch options so the dominant ones can't own it all. As for getting her to be less dominant, I don't know what you could do, really, except maybe two things. One: get a feisty hen who will beat her up and change the social structure. Not that the pekin may back off the others even if that happens. Two: shackle her. Sometimes I do this with birds that are aggressive to others to an excessive degree and are willing and capable of harming them, namely turkeys. I have never done it to a little hen though, it could lead to her getting beaten to death. I've only used this when introducing a turkey, for instance, or a bird that won't get bullied, to a flock it has shown tendencies to be too aggressive to, but will be living with in future. Also when travelling a turkey hen with another hen she loved to beat up. Now even the feel of little anklets calms the savage beast, I no longer actually shackle her. She used to be a chronic to-the-death type bully given a chance.
What I do there, not that I actually recommend doing it to a pekin hen, is to get a soft, thick but fairly strong piece of rope of cord and tie it around each ankle, making sure that it is loose enough to slide up and down the leg between knee and ankle freely, but not loose enough to slip over the foot or up the leg past the knee; it also has to allow a good stride, the same amount as her normal walking, but will prevent her chasing another bird. You need to be very careful if you do this; watch that it's not slipping tighter or looser, make sure the knots are good, make sure she's not in an area where she can get caught on anything, and watch that the others don't suddenly want to kill your newly compromised bully. Personally I think that if your rooster doesn't get used to her the way she is she will either end up a reject or dead, or maybe you'll just have to get used to her the way she is... If you're not willing to try the other options I named, as in rehome her or get her starting her own separate flock, or whatever... Maybe over time she'll settle down anyway... Good luck with whatever you feel is the right decision.
