Michael does indeed continue to make undesirables disappear after coming into contact with humans. Right after the Church of All Worlds goes into hiding, he disposes of a couple hundred people whom he deems not safe, because it’s better to kill a man than to imprison him. As he puts it, “for a while, this will be an uncommonly decent city.” He doesn’t do it when being martyred because he goes out to meet the crowd on purpose to have them martyr him. (Yes, he’s shot a couple of times, then pulled apart and incinerated.) Remember that according to his worldview, he can’t die–all he was doing was discorporating and thus making a powerful symbol for his religion.
“Feminist chauvanist” I can buy, but “strong female characters”? Let’s take a look at the examples you cited. Friday is emotionally dependent on and a tool of RAH’s favorite character, the Wise Old Man Whom Nubile Young Things Would Love To Have Sex With. She’s neurotic. But she’s the best of the bunch, yes. Eunice (IWFNE) is the Wise Old Man, who’s taken over the body of the Nubile Young Thing. And both before and after the merger Eunice’s main source of power is that she’s sexually desirable and thus can make men do what she wants. This is also true of Maureen in To Sail Beyond the Sunset. Finally, the women in TNotB are both intelligent but control the men largely by sexual manipulation and temper tantrums. The women are all intelligent, but contrast their behavior with that of the men in the stories and you’ll see how they use sex to get what they want when the men use force of will. If those are strong female characters, I fear to think what weak ones are like. The strongest female characters he’s got are probably the ones in Tunnel in the Sky, and even they are generally–not entirely–subordinate to their male counterparts. RAH is a 1960s male feminist: women should be intelligent (so they can help) and sexual (so they want to sleep with the men) but they’re still fundamentally beautiful children.