Well, I believe that it is already being done: there are clubs in the US that do not accept African Americans or Jews.
I worked for a company owned and operated by the Episcopal Church. There was an explicit statement in their Guidelines that the company reserves the right to limit certain positions to Episcopalians. From the outside, it seems very discriminatory; but you had to have worked there in order to understand that this is not really an unreasonable requirement.
In any democratic, multicultural society, a balance of needs of the various individuals needs to be achieved. This balance, for lack of better criterion, has to be based on the will of the majority, IMO. Therefore, if the majority of the Israelis believe that discrimination is a more dangerous foe than infringement of the rights to Free Association, it's a valid choice. In the US the situation is different.
In addition, these things work both ways: if the gentleman in question believes that the Boy Scouts rules are discriminatory, and there are adequate numbers of people who believe likewise, then he is free to start his own group, which will have the attributes of boy scouts, without the requirements that he finds offensive.