Honestly, I think you may end up with the best of both worlds.
When I lived in Korea, I mainly lived in Seoul and Kangwon-Do (춘천, 원주). But I always wished that I had been able to pick up on more of the southern dialects. By going to Pusan, you have a chance to do this. Since you are going to a language school, you should be fine in learning 표준어 (standard speech). But you also get the flavor of learning some dialect.
I should also add that Pusan is of course a rather large city. Not everyone there is even from Pusan (or 경상도 in general). You should get a decent mixture of dialect there. It is a little bit like if you lived in Atlanta, Georgia in the US. Not everyone there speaks like a southerner.
My guess is that you will be just fine learning Korean in Pusan, then looking for a job in Seoul.
Lean more heavily on what you learn in the language school for formal settings, but have fun with learning the 사투리 as well.
If you are interested, you can look up a man by the name of Robert Holley (Korean name 하일). He is an American who has learned the Pusan dialect, yet still manages to be very successful nationwide. (I heard him on the radio once and thought he was native Pusan)