There are plenty of examples of engineers that make terrible managers, to be sure. But there are also plenty of examples of managers with business backgrounds that have absolutely no idea about the consequences of their decisions. An optimal result requires skill in both domains.
By this point, you might be thinking, "Hey wait, isn't it true that cost-cutting also had a role in the crisis? Wasn't there at least one engineer that sounded the alarm in a memo?" And my answer to that is a resounding yes. But the question remains, where the hell did that idea come from? At no point did anyone think, "I'd love to spike my profits this quarter here and have huge disaster that will tank us in the next quarter." Therefore the problem isn't one of simple pursuit of the profit motive, because it is quite clear that Boeing hasn't profited from this situation long-term. And that's why I have focused explicitly on this foolish, self-defeating management fashion at the top of my mini essay here.
This brings us to the topic of Boeing's future. I could be wrong about him, but the fact that they have selected a person who majored in accounting to be their new CEO does not bode well for them. At the very least he has a major gap in his background to overcome, and at best I can only see them just managing to hang on instead of growing.
How does this relate to the merger issue? This management fashion I am speaking would have likely infected both McDonnell-Douglas and Boeing had they remained separate. That's because companies hire people out of the same pool of people that learn this stuff in their universities! Maybe there is a case to be made that having separate companies would make it slightly harder for them to both fail, but I believe that this isn't a very strong argument.