Each string fits into the nut slots at an angle. Doesn't that mean the red edge of the nut (see picture) is the only thing that matters for holding the E string in place? Similarly, isn't the pink edge on the nut responsible for holding the D string in place?
What I'm getting at is if I file only the "unimportant" edge of each nut slot (green and yellow edges in the picture) wouldn't this accomodate a higher gauge string without allowing it to swim as you said?