While the "leave them and let them sort it out" sounds great, the truth is the pony can be severely injured by this mare. And she can go down and be hurt too, in the mud.
And him going in the shelter is a great way for her to pen him up where he can't get away, and end up kicked to death too.
At this point? I'd separate them. And keep it that way.
Mare will more than likely not stop, for that matter. I've seen horses like that, and have seen them run one through a fence too.
Horses make me a better person.