Much is being made about capacity and cost. The assumption is that the iPhone 6 will be ONE model and it is an all or nothing proposition for sapphire.
Much like the iPhone 5S and 5C models, I envision a premium model costing hundreds more WITH the sapphire screens and certainly other upgrades, as well as a lower cost option WITHOUT sapphire for a broader customer base.
This allows for the arguments regarding capacity ramp in Arizona to be moot (if capacity is indeed limited at launch - some argue otherwise) and only limiting customer choice and not limiting customer access to the iPhone 6. It also makes the cost issue moot as it allows the customer to choose whether they pick the premium package including sapphire along with the added cost, or the more basic model.
As a side note, some argue the cost difference between GTAT sapphire and GLW glass is dwindling: http://seekingalpha.com/article/1957211
I can agree with your message here. I'll be one of those paying up for the sapphire, if (and only if) it doesn't sacrifice structural integrity to gain scratch resistance. In other words, if it shatters more easily than Gorilla Glass, then count me out. I want it all if I'm paying more $$.