Disclaimer -- please do not take this the wrong way, I'm just trying to get a feel of what the anti-greek people are feeling.
My older [biological] sister attended and graduated from A&M, and even though I only went to visit her a few times, it was enough to see how much the students love their school and it's traditions. When I was in high school, I went to visit her for the last bonfire that burned and I was amazed at how wonderful the comraderie (sp?) was between the students there.
I don't go to school there obviously, so I can't say for sure where the anti-greek sentiment stemmed from, but most of the anti-greek stuff that I have heard comes from greeks scheduling their social events on big Aggie tradition days -- like the Silver Taps day that the thread you linked to refers to.
Another incident I can recall is the panhellenic bid day scheduled on another Aggie tradition day (although I cannot readily recall what exactly that day was?)
And supposedly the Greeks there use publicity tag lines like "Aggies First" and that is where the problems begin -- when they claim to be "Aggies First" and then schedule things on traditions. I have friends who also attend A&M and they have nothing but love and pride for the school they attend and the traditions they try to carry on, so that is what bothers those people the most.
And I would guess the same would probably hold true for any other university that has such a rich history and traditions such as that.
I think all the bad PR could be avoided... But that's just my .02
