It's funny. It's supposed to be funny. It is supposed to be collectivist because a unitary subject makes it funny. Twain knew it didn't apply to everyone, that is why he wrote it - to wake people up to their "sheepness", to make them question their leaders, political and religious.
Basically, chill out and try some reading comprehension.
You said: "In addition, many of those who do the invading have been lied to and fooled, being told that what they were doing was stopping some great evil or another." -- Exactly!! Well done. Twain wants you to question.
My only critique, you said: "you cannot blame religion for it any more than you can blame atheism." --- Yes, Yes we can. Many wars have been fought and many genocides have occurred for purely religious reasons and no other, and by that I mean the people doing the fighting were doing it as a religious act, no matter what those and power had in mind. The Crusades, the Inquisition, WWII (The Germans), Pol Pot, Mohammad's conquests, and, yes, our current "War on Terror" just to name a few. And no, atheism cannot be blamed for any atrocities, it's never happened.
Then you said: "How many religious people have devoted their time and energy to helping the poor, the sick, the orphan, the widow?" -- Who cares? That is a logical fallacy of apples to oranges. It has zero to do with the subject matter of violence for religious reasons. And I guess a more direct answer to your questions would be "a very small percentage" from what I have seen in my life. Even Mother Theresa did nothing to help the poor and the sick, she just made them feel better so they could die happy.
"In the beginning of a change the patriot is a scarce man, and brave, and hated and scorned. When his cause succeeds, the timid join him, for then it costs nothing to be a patriot."--Mark Twain