Jill the dam is always the best solution, so if she will let him nurse, even if you have to be there, that is preferred.
One thing that may be happening is that with the prolapsed uterus she maybe having more pain than normal when he nurses. You might consider Banamine once a day for a couple of days and seeing if that helps her.
Also, Bag Balm does wonders if she has sore nipples. We use this on all the mares at about 6-12 hours after foaling as that is when they get sore. Colts are more aggressive feeders than fillies and he may be being a usual colt, but it is hurting her more.
As you have already discovered, the more room you give the colt to be able to get away from her the better. Avoid tight areas.
If he runs away does she follow him? You want her to bond with him. So if you can lead her away and he will follow and vice versa, that is a good thing and you are on your way.
When we have had problems I milk out the mare and feed the foal the milk from a margarine container held folded into a V. Giving the foal moms own milk does two things, it drains the dam's full udders and minimizes mastitis and gives the baby the formula that he should be eating.
I hope this helps you Jill.
I'm relieved to read that your mare is getting better with accepting her new baby.......
Joanne's post makes a lot of sense to me. Early on, the nursing can cause a major reaction to the mare's uterus with contractions. So if your mare had a prolapsed uterus, there may be some painful reactions occurring...... I agree with the suggestion of giving your mare some banamine for a couple of days to see if it makes a difference. (Check with your vet, of course, as well.)