I just went through the same thing. My mare and gelding have been together (but in separate pastures at boarding facilities) since he was born. 11 years later we finally bought our own farm last year and they have been here together since Feb. They became attached at the hip although my gelding has always remained alpha.
Last month we got a companion pony mare so that if I have one out vs the other, the horse left behind would still have a buddy. My gelding hated the pony. We even aced him the first day they were fully together so he couldn't run after her and had to get used to her. Everything seemed *ok* and she had a few nips here and there after a week, but nothing major.
He kept keeping my other mare away from her though and started protecting the field. We went out one day for a few hours, came back and the pony was standing in a corner of the field. After 15 mins she was still there so I went and got her. There was evidence that she had gone down (mud on her hip) and he grabbed her by the crest of her neck. Thank goodness he didn't do worse.
For the past 3 weeks now he's been separated in his own field and the two girls are together. They like each other, he seems very happy and content that he doesn't need to protect anyone anymore and all is well. I only have 4.22 acres, but it's laid out very well so they all have room. I do want to build another shelter at some point, but until then he can use a paddock that has one on bad days.
On a positive note, him and the pony have been nuzzling and grooming over the fence so it may just be that my boy needs more time getting to know her and see her there before introducing. They were over the fence for a week prior to me putting her in with them, but that may not have been long enough for him. Maybe it's the same with your boy? Maybe he just needs more time to adjust with him on the other side.