I mean, tinfoil answer is because they're cheap, and the cost to rework sounds like a motive to me, frankly.
Boeing likes spending money on rework so they knock off someone ratting out their key supplier because they want more rework? What?
Also they don't use Spirit because they are cheap, Spirit is not a cheap supplier. Boeing sold the contracts with that chunk of the company when they sold it. Further, Spirit is basically the only place in the world that could do this work today, they have 13M square feet of high bay, fully environmentally controlled manufacturing space including over a million square feet of clean room space. They have been building the components they build there for decades.
Over the years there have been publicly known quality issues from Spirit that have resulted in missed deliveries and airworthiness directives, why would Boeing not kill anyone over that, but kill someone over ratting out what appears to be less serious problems?
I think it's possible that some random guy got sick and died, than the Clinton's are knocking off anyone that says anything negative about anyone connected with Boeing.
BTW: Spirit also makes stuff for Airbus and Gulfstream.