> does anyone think that this was the intention behind these agreements?
Absolutely.
> Isn't it more likely that ...
This is a just-so story.
> It would seem as though ...
All companies are vulnerable to losing key employees. There are two ways to address this problem: (1) do good, legal things to address it (2) do bad, illegal things to address it.
I mean, to use a perfectly ridiculous analogy, suppose for a minute that engineers are cards from Magic: the Gathering and that CEOs and their executive teams are the players. A CEO can probably count on the loyalty of their inner circle. Or at least I would hope so. A CEO with a disloyal inner circle is going to be toast sooner rather than later. But generally speaking you can't count on the loyalty of engineers. They care more about the challenge, the money, the excitement, being a hero, being a rock star, etc... and the high-level ones tend to act like rock stars (not all of them by any means, but a substantial and vocal minority). These are the "rare" cards in Magic: the Gathering. They are super-valuable and they can make the difference between winning and losing.
Now imagine playing this card game where the cards have minds of their own. We can sorta rationalize an anti-competitive agreement between the players, a prohibition on poaching each other's engineers, product managers, designers, etc... because the players all want to play the game a certain way and don't want the headache of dealing with brain drain. They rationalize, "it just makes playing the game a little bit easier and allows us to sleep at night". The problem is that in the real world, it is real people who get hurt when these kinds of agreements get made. Doing this is not only illegal, it is wrong. You're creating an agreement that essentially says, "these engineers are my property, those engineers are your property. We agree to not steal each other's property."
By making such an agreement, you're intentionally depriving another human being of a legitimate economic opportunity. You're saying to them, "I'm going to deprive you of an opportunity for my own benefit, and I don't care about how it affects you or your life."
I find this sickening. You might as well say, "I'm going to sacrifice your happiness to increase the size of my bank account". It is a form of exploitation. I mean, I'm a fire-breathing free-enterprise capitalist, but the Marxist line of reasoning about exploitation and alienation rings true on this one. The problem here is that free-enterprise principles are being violated.
> The result would be a destruction of value
Perhaps, but I can use a similar style of argument for the opposite conclusion. If a few key employees would have gotten substantially more money, then you would see those employees, as a group, making different decisions. They might have gotten together to create a new innovative company in which they were much more personally invested. It is possible that huge opportunities for value creation have been missed and can never be recovered.