how are they supposed to keep that from happening, though? give someone a higher/lower seed that they don't deserve just to keep them from playing a conference opponent again? that would be ridiculous. and unfair.
the only deviations by the ncaa in seeding order from the ita rankings were flipping stanford and baylor from 7/8 to 8/7 (understandable, given baylor's 4-3 head to head win during the season) and flipping kentucky and georgia from 11/12 to 12/11 (understandable, given georgia's home court advantage and a 4-3 head to head win during the season).
granted, these two minor changes did result in 6 of the 8 sweet 16 matches being conference repeats, as opposed to the 4 out of 8 it would have been if the ncaa had gone straight up with the ita rankings. but does that really make that much of a difference? not really. and it's basically just coincidence anyway, it could have been the other way around if a couple matches would have gone different during the season.
that's just what happens when the big 5 conferences (sec, acc, big 10, pac 10, big 12) dominate college tennis like they do right now. there's really no way to change it that makes any sense, or is fair.