The problem with the Vong is that they're indicative of a fundamental misunderstanding most of the EU authors and publishers laboured under almost right from the get-go. That being the notion that Star Wars is science fiction.
Star Wars is space fantasy, so many of the standard sci-fi tropes aren't entirely compatible, at least not without some adjustments. Star Wars is an entirely different animal than the likes of Star Trek.
First-off: yes I know: space orks = space fantasy. At least in theory. In practice that was purely superficial and not at all how they were used. They were just straight-up alien invaders with a very thin veneer covering the real word religious allegory. They were closer to torture-porn obsessed Klingons than anything.
Secondly: the idea of a horde of rampaging aliens is absolutely doable in Star Wars, but the execution was all wrong and the resolution and aftermath was pathetically weak.
I don't think it was trying to portray him as Benevolent, he was trying to protect himself.
Intended or no, that was the logical implication. Whether or not they thought through the implications, it fundamentally re-contextualises *everything* he ever did because it's altering his base motivations. For example: Death Stars are suddenly not tools of oppression and dominance but sentinels to protect the peoples of the galaxy from extra-galactic marauders. Which in turn means the heroes have been actively hurting the galaxy's defences and undermining it's unity in a misguided attempt at imposing freedom.
It presupposes that an authoritarian rule is justified in any excess provided it's purported that it's the only thing that can protect the people from the barbarians at the gate. That's very dangerous ethical ground indeed.
Also, there are much easier ways to deal with that situation in a selfish way. I mean the galaxy is a *huge* place. Running and hiding somewhere in the deep core is perfectly viable. Also, as the article points out, if Palaptine really had known about them and did what he did specifically to counter them then his propaganda machine would be shouting it from every rooftop. Totalitarian regimes don't just love a perpetual external enemy, they *need* them to stay in power over the long run. The Vong are the perfect bogeyman with which to terrorise the citizens of the Empire to give up all their personal freedoms and rights in exchange for protection from extreme-bondage vampires.
In short: the concept just doesn't hold water.