I was actually in a similar situation when I went through recruitment. There was a group of four of us who were all best friends and we all wanted to be in the same sorority. But, during recruitment we realized that we were four different people with four different personalities. I went ZTA, my best friend since the fourth grade went KD, and the other two both went Tri-Delta. But, one of the girls went Tri-Delta cause the other one did although she really had her heart set on KD. A year later, she disaffiliated from Tri-Delt wishing that she had made a different choice (Tri-Delt happens to be very good on our campus...nobody twist my words!
But, she would've fit in better somewhere else) Are we all still friends? Yes we are! I actually ended up moving in with the two Tri-Delts (I'm still friends with one of them but the other one...eh...we're not friends do to roommate problems and NOT sorority problems...word to the wise: NEVER move in with a good friend!). So, it is possible that you and your friend go to different sororities and still be best friends. It happens all the time actually. There are many girls that were in my pledge class who came to rush with their best friends and all went into different sororities. You have to find what's right for you...not what's right for your friend. Also, things happen during rush week. She may have gotten cut from the sorority you have your heart set on and that you know you'd fit perfectly in. Don't let your friend make the decisions for you!