Horses don't have the emotions attached to reproduction like humans do. I don't believe they have a concept of "rape" and can't be traumatized like a human can in that manner.
If the mare cannot have a follicle fully develop to the ovulation stage, then hand covering her, with or without "force" (which I assume to mean hobbles, sedation, or other restraint) won't work anyway. In order to manipulate her to reach ovulation, you would need to administer the correct drugs/hormones under a vet's supervision and have access to an ultrasound to monitor her progress. If you plan on doing that then AI of fresh semen would probably be best.
I would have the vet check for hormone imbalance prior to trying too. It is possible she isn't producing the correct levels with only one ovary.
If none of that is the problem, maybe the stallion is too aggressive and she is reacting to his advances in a fearful way because she doesn't understand what he wants. Maiden mares (and some mares in general) don't always have the instinct to stand for mounting. It really is safer for everyone to do AI. When that is not available, you have to think of the handlers' and the animals' safety and determine whether physical/chemical restraint is enough, or if the breeding should be rejected. As a stallion owner, I don't want to take a kick and I certainly don't want my stud to either just as a mare owner doesn't want her mare injured.
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