The PRISM slides list per company agreement dates spanning over five years. Microsoft started first in 2007, Google was added in 2009, with Apple being one of the last in 2012. If it was a system that was simply ingesting FBI data, why would it wait until 2012, unless you're suggesting that Apple didn't respond to FBI requests at all until late 2012?
Just because the NSA had a program to exceed even what had been negotiated via PRISM, doesn't mean that PRISM didn't involve collaboration.