As an Orlandoan with a few friends in that community, I don't think "religion" was the real factor in the pulse shooting, but self loathing homophobia that was exacerbated by religion. Couple that with the teasing of his co-workers and government meddling in his life due to false claims of terrorist links being investigated seriously, it makes sense that his self loathing rage manifested in a public and destructive way. It'll take alot of serious evidence to convince me he has any link to any terrorism or that he did it to send some religious message.

As a brown man I look into these things pretty seriously so that I can defend myself against slurs and idiots. Pulse hit particularly close to home as I was driving through downtown Orlando on the highway at 3AM that night and saw about a dozen cop cars from western counties streaming in. Then seeing that the shooter was a brown man born in NY a few miles from where I was born and that he'd randomly wear a Yankees hat like me. He also scoped out an east coast gay club where my friend DJ'ed.

Most religious people of course think that their religion is what they believe. So if she is a Muslim and sees the (for her) good things in Islam, clearly, it is hard for her to see how a terrorist who kills innocent lives could be a Muslim.
Objectively of course, both, the terrorist and your friends are "proper" Muslims. they just chose to use an irrational believe system in very different ways.
I oppose all religion and I am probably more and antitheist than atheist but I still think it is wrong to think that religions are some specific static constant believe system. that is not how it works -- there are endless variations, sects, subgroups, cults, and personal interpretations of each religion and to generalise over all people who call themselves Muslims or Christians or Hindu etc. would just be silly and damaging.