if its a manual, then there should be an equaliser hose that you can get that connects the two at the fillers. And it doesn't really matter that the two mix because the levels will remain generally correct. But if its an auto, and the fluids are different types, then you may need to look at getting it replaced. And if thats anything like the manual, you may as well recondition the whole lot while your doing it, cause you have to pull the lot out.
The seal is fairly easy to change but there is a lot of labor($$$$$) if some one else does it. While everything is apart do a recondition/rebuild. I do not think you will save money by just fixing the one problem, the other seals bearings etc. will pop up just because Murphy makes them.