Pyramid schemes necessarily involve fraud, particularly assertions about a products quality, or market penetration, or underlying value.
Not necessarily. There were several pyramid schemes started here on this forum which were quite open from the beginning: you pay X to enter, you receive a certain percentage of what people after you pay etc. No fraud involved.
Luke-jr used the result of peoples computing power, not the power itself. Why is this distinction important and is it actually a distinction? People who signed up with Eligius did so in order to mine Bitcoins. Merged mining involves no additional work in order to function, it uses the results of other proofs of work in order to build its own blockchain. Luke used the results of the BTC mining to attack CLC. Eligius users would earned the exact same number of BTC had Luke-jr not attacked CLC. Since nothing was taken from Eligius users, no economic damage occurred. Eligius users did no extra work to take part in the attack on CLC.
I understand how merged mining works and that it costs nothing extra to miners. But it doesn't matter, I don't believe you can say that miners are giving "full authorization" to pool operators to do whatever they want with their calculations. It's as if your neighbor borrow you a knife for some cooking he's intending to do, and ends up also using this knife to harm someone. Or even to do something not criminal but that you personally don't agree with and that was not clear from the start, like, I don't know, torturing/killing his own dog or something. The fact that he returns the knife intact to you (no lost) doesn't change the fact that he betrayed the implicit agreement.
Should a crypto coin with such a deep structural flaw deserve to survive?
What deep structural flaw? I mean, bitcoin itself could receive such attack, by someone with much more processing power. This new coin was on infant stage and obviously could not counter Eligius attack, as there's no other big pool honestly mining it AFAIK.
The entire premise of cryptocoins is that they are immune or at least very resistant to such manipulations as occurred with CLC.

The only known way so far to resist a >50% attack is by centralizing the network.