No, I don't think he's afraid of violence by Muslims against Americans. He's afraid that any initial acts of violence by Muslims against non-Muslim Americans will generate reprisals that will compicate diplomacy overseas.
Imagine the response in the Arab world to hundreds of Muslims in America seen hanging from lampposts
Now reread what you wrote - 'violence against non-Muslim Americans will generate reprisals that will complicate diplomacy overseas'. So you are saying she is essentially correct - he is afraid of violence by Muslims. That is why he went sock-footed to the mosques, had Ramadam celebration in WH, preached tolerance and threatened Americans, insulted the Christians, etc. He is afraid of them. "Complicate Diplomacy"? Well, I suppose if you think Americans fighting back would 'complicate diplomacy', you are probably right. What do you think the President would respond to Americans fighting back at terrorists?
You have brought me closer to her way of thinking than I was - and it is chilling.