Pinning it on a culprit - the one villain - clears everyone's name, and gives media fodder for headlines along the lines of "the hijacker and his dog in 2005!". Boeing, the Malaysian officials, lots of stakeholders with every interest in that being the outcome. I actually wonder if the Malaysians want the aircraft found at all.
Boeing though will walk through it professionally - they've been through enough air incidents to know this dance. They won't try to cover up, because as you point out, the information is already out there. I'd say also for every Boeing issue, there's an Airbus issue, and the airlines all know this.
As for 45,000 feet - I'm leaning towards a hijacker (or team) from outside the cockpit, with adequate knowledge to operate the flight management computer, and potentially a subtly unco-operative pilot who knew FL45 might starve the hijacker of oxygen. I think the vertical deviances are amateurs-in-charge.
But then, nothing is clear in all this.