Your list of flaws made me realize some other flaws as well.
I mean, he said that the best way to PROTECT their mission (from what?) was to speak honestly about it (WHAT??), because no one would believe them, and they would be locked up in a mental hospital, medicated to madness and then killed.
Ok, I added the last part, but isn't that what he is ESSENTIALLY saying?
Wouldn't the BEST WAY to protect the mission to just 'blend in', and appear to be 'normal' to everyone else, and never mention the mission? That way, no one would know the mission (how is explaining the mission honestly even protecting it? I mean, what about 'explaining the mission honestly' actually creates any kind of protection? How does that work?), and no one would know to attack them or whatever.
Just keep it secret, don't mention it to anyone, and behold; you need NOT be in a mental hospital! Wow, what freedom, just by that simple thing.
So his logic certainly wasn't logical, or his delusion "perfect" by any means.
Also, it's not 'rational' to help others, it's 'sympathetic', and you need to feel to do have motivation to do it. Of course technically you can help others without feeling anything, but that whole thing was quite odd anyway.
From all the UFO books I have ever read, the visiting E.T.s have always been shown to have lots of compassion, love and caring for the fellow man, even if the fellow man is an odd Terran half-animal that creates only war, pollution, destruction, murder, chaos and ignorance (the point about stupidity is quite good, though, because against it, even the gods are said to be powerless).
In any case, it's just another dull, depressing, grey and lifeless movie that shows the limitations of the terran denizens. They can't even grasp who or what they are, and yet they try to depict stories of visitors from other planets, who supposedly understand a lot more. It's very clichéic, and not very imaginative.
I have read better stories in comic books. There exists a plethora of good stories in sci-fi books, and the reality descriptions in UFO books is fascinating, no matter what your stance of their truth might be. If you read the texts that have allegedly been 'channeled' from E.T.s, you can find deeper wisdom and better understanding of the human nature, the human soul, and all the philosophy that was touched in this movie than the movie itself ever even knew what to do with.
My point is, that there are so many better E.T. visitor-stories out there, that there's no point in wasting time with this depressing and imaginationless, dull and mundane crap.