To be honest it sounds like he is being very childish. I suppose it depends how deep 'didn't get on with at college' runs and the reasons behind that. If it was just a personality clash then he should rise above it and step out of the playground - if it was something more personal then maybe he genuinely and reasonably has a dislike for this guy but either way, to threaten to kick someone's head in at your wedding is wholly unacceptable. It's adding extra stress to you as a couple and he'd get short thrift from me as a WP - it's my job to protect couples from these sorts of things and he'd feel my boot firmly on his butt!
In a nutshell (and without knowing all the facts) his behaviour is unacceptable. If he had come to you calmly and given a reasonable explanation for some genuine concern fair enough but I can't imagine any reason why the seating plan should be changed.
Perhaps the question should be, is he the right person to be BM and seated in a place of honour at the top table? Perhaps he would prefer to relinquish his BM duties and sit with his GF on a different table.
I suggest you identify the real reason for this dislike and if it's simply the BM being ridiculous then tell him to go boil his head!
You could of course call his bluff and say 'okay you sit with your GF and we'll put OH's cousin on the top table". See what he says to that!
Good luck x
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