Abe,
You bring up a lot of points!
The Buddha's teachings were misunderstood as nihilism from the beginning. There are many discorses where again and again the Buddha patiently pointed out that he taught neither nihilism nor eternalism, but instead the four noble truths, or dependent arising, and so on. Have you noticed this, too?
Secondly, as you observe, the liberating teachings of the Buddha have been and continue to be used to dominate people. That tells me a lot about humanity. I would not draw any conclusions about the Buddha's teachings from just this, however.
Thirdly, awareness of one's mortality is simply the prudent way to proceed, and is not limited, as you yourself write, to Buddhism. It's the one thing we're absolutely certain will happen to us. We make preparations for all kinds of eventualities, but death we (as a culture) tend to push aside. What's unhealthy about being prepared for the one event we really can be certain of happening to us? Also, I myself find the idea of an immortal soul rather disheartening

Four, the "life has no reality ..." quote you criticise as being insufficiently uplifting. The thing with being uplifted to a peak is that the peak moments are so rare, and descent invariably follows: to demand only peak moments is just not realistic.
Five: the existentialists, especially Camus (who did not label himself existentialist, BTW) have "independently verified" a lot of the things the Buddha described. The Absurd fits in nicely with the three characteristics, in my opinion. I'm not sure how you want the "religioin for atheists" remark understood, but atheism and nihilism are completely distinct concepts.
Cheers,
Florian