While technically the RSS may have a Muslim wing tucked away somewhere with some token members, it was, is and will remain the umbrella organization for advancing the Hindu (religious) viewpoint. It has been violent many times in its history, and even today stands accused of engineering everything from riots to bomb blasts. And always with an anti-Muslim agenda.
Mind you I'm not saying Modi will follow the RSS agenda (I don't think he will, he's far too shrewd and smart for that. He will not compromise his ability to stay PM for 10-15 years for short-term Hindutva agendas).
A former colleague of mine just wrote a magisterial account of the RSS' history and future in India for Caravan magazine. I'd recommend those who want to understand more about RSS, BJP and yes, Narendra Modi too, give it a read at leisure. It is a long piece.