Same thing happened to me and one friend in particular. She was kinda dumb--I wore my pledge pin around her during my entire NM Education period, and she didn't notice. She would complain about how everyone in fraternities and sororities were wealthy, spoiled athletes, and how they just wanted me because of whatever stupid reason she could come up with. She eventually found out and got over it. My other friends were supportive, they aren't the types who want to go to fraternity parties, but they are very open and supportive about it. I'm also seeing someone who is against the Greek system, but is supportive and is willing to go to my semi-formals and crush parties with me!
It probably helped me that I have many friends (not from college, but from high school) and family members who are greek or supportive of the Greek system.
If they are your true friends, they'll get over the shallowness of their arguments. You'll do what's best for you.