I've had a few jackets altered for the shoulders. It should be no problem to take out the shoulder pads, but I think that will make the shoulders go out even more since they won't be propped up by the shoulder pads.
I would take it to a seamstress and ask her how much work you are looking at...I bet they can make it just the way you want!
they should be able to take the pads out and then take up the arms at the shouler, which will bring it in to your natural shoulder. It will make the sleeves slightly shorter though.