I'm pretty familiar with how all this works on the FDA side with medical devices/software.
If it's the same general setup as on the medical side with the FDA, then it's a virtual certainty that liability will fall with some compliance and QA types, as well as any engineers or engineering managers who signed the relevant documents. Those signatures are all legally binding, and represent to everyone up the chain that the systems in question are functioning properly. If the government can show that the systems in question could not have been functioning properly, they got you. (Another thing we learned from our lawyers about the FDA side, each document that you signed, represents one count of lying to the federal government at a minimum. Multiply that by the number of documents signed to get a single system through, and you get an idea of why you should never sign anything if you have any reservations at ALL. No matter how slight the reservation. No matter how much pressure the higher ups put on you. I think the rules are the same on the FAA side. So these guys have really stepped in it.)
That said, they may be able to snag a few executives here or there, but only if they can prove who knew what, and when. Execs, you would think, would be pretty careful about liability type things, so they could look very hard and not find anything on any of the execs. It would not be collusion or preferential treatment, it's just hard to find that kind of a smoking gun in a mountain of electronic documents and messages. (I strongly suspect that if the government were to press hard enough though, that some of the engineering managers and compliance types would turn state's evidence to get lighter sentences. At that point, you could probably get some execs I'd imagine? Still might be hard though.)
The engineers and QA/Compliance folks, though, should really be consulting with outside counsel. Just as a precautionary measure. I wouldn't trust Boeing execs to not throw me under the bus.
And this time around, it looks like a pretty big bus. I don't think you survive this hit.