I am certainly not a tax pro, and wouldn't want anyone to act on my comment - but just my perception here:

If I pay someone $100 in quarters, and receive $100 in bills - and then take $50 in the bills and donate to charity - my donation is $50, not $50 minus the $50 I kept. The charity did not give me back the $50, just as this charity is not giving back the miles in exchange for the magazines.

So, whether or not one should deduct the value, or whether or not it is acceptable to the IRS, I don't know. But I don't see how the value of the miles should be taxable. They were not earned, anymore than they would have been earned if they were just purchased directly from an airline or hotel.