To answer your question in order of their appearance:
Does "are not to be accepted" mean "won't be accepted"?
In short, the answer is no, they don't mean the same thing. As StoneyB mentions in their comment, the former is a statement that an obligation exists to perform an action, while the latter states a prediction of an action occurring.
What makes "won't be accepted" different?
Essentially, the difference is between obligation (are not to be) and prediction (won't be). To combine them in an understandable sentence, take the following:
Broken or ripped dollar bills are not to be accepted as payment, but that doesn't mean I won't find some in the till at the end of the night.
That sentences states that there is an obligation not to accept ripped dollar bills, but predicts -- in negative language -- that some ripped dollar bills will be accepted in defiance of this obligation.
Why did the author use [are not to be as opposed to won't be]?
Because the author wanted to convey the obligation. As the author states elsewhere, publicity has shown such discrimination does exist and is practiced (so predicting it not to occur would be either wrong or a lie); the author is trying to make the point that it shouldn't happen.