You need an anti fungal really to kill mould spores, so technically tea tree could work, but I suspect that you'd have to apply it neat every day for quite some time to get rid of it, and I wouldn't be keen to rub neat essential oils on the rubber seals on my windows!
I know its not eco friendly but could youy use a solution of Milton to clean it all down with now to get rid of it?
Then I find wiping around the seals every couple of days gets rid of any moisture there and prevents the black mould stuff growing in the first place

Milton is great for killing mould spores! The prob with them is that you can wash them off the surface but unless its anti fungal you use they will keep growing back again.