I think it would affect some proteins, but ammonium sulfate precipitation usually requires such large amounts of salt, that you would have to add a _lot_ of base to adjust the pH.
When I have done ammonium sulfate precipitation, its to take a rough cut of proteins out of a whole cell/whole organ lysate - its more like a hammer than a pair of tweezers as far as protein purification is concerned. I would rather use a charged plastic resin or a sizing column if I were to care about the isoelectric purification.