Best Buy will honor Student Discount, you just have to work your magic.
Here's my story of when I purchased my 2010 MBP 15 inch. (When they first came out, not when they offered the MBP + iTouch for school a few months later)
Here's what I did.
Did my research, found that Apple did in fact do the Student Discount on the new model. I think it was $200 off at the time. Price was $2,199 and with student discount it was $1,999.
Called my Local Best buy, asked a sales rep if they price matched, he put me on hold, asked his manager, came back and said no.
So, then I called another Best Buy, 30 minutes away from me, but this time I went about things differently.
When the sales rep answered, I immediately asked for a "supervisor or manager" the sales rep then asked me if he could help me. I kindly said sure. I then proceeded to tell him my entire story of what was going on, why I wanted to buy it at best buy and not apple, etc.
I said something like, "I want to purchase the MBP at your location because #1, I want to finance half of it with my Best Buy Credit Card (18 months no interest), #2 Because I WILL be purchasing your $350 3 year, insurance. #3, I am a loyal Best Buy Customer, (Silver Member in Best Buy Rewards) and I would like to add more "Points" to my Rewards card.
I then told him that I WILL be purchasing this TODAY from your location if you price match, and that the simple price match of $200 is determining if you will get a very big transaction. I think it was around $2,550 with Taxes.
If they said they would price match, I would get it from them, if they said they wouldn't I wouldn't get it from them.
The guy was very nice, told me he would tell everything I told him to his manager. He put me on hold for like 5 minutes. Came back and said his manager approved it, asked for my name, and put my Brand new MBP on hold until later that afternoon : )
So now I have my new MBP, and my 3 year, Accidental warranty that covers everything from Liquid damage, to damage from falls.
Just be persistent, keep things in your favor, don't act desperate. Say you will only get it from them if they price match. If your local store doesn't call another Best Buy and try again!