That's since Ageira is not looking to start a head-on fight with the larger pirate syndicates.
And if you read carefully, general pirates are not treated the same way.
They have to drop the cargo, or die. If they drop the cargo, and it it still permissible within the bounds of the Ageira ID, they may still be attacked/and or killed. (We have permission to hunt Pirates and Hackers.)
When writing this, I wasn't actually considering the situation with Gallia. There are Junker-killing missions available on Ageira bases. Many corporations don't like the Junkers; most see them as scavengers, so if they've got Parts, it indicates they've gone out of their way to steal our product.
Also, reading the linked post about Ageira bounties, go to the end and notice the screens of an indie Junker hauling Parts. While you may claim that's simply one individual, we're not taking chances.
As for Gallia; I like to say that Ageira strongly suspects the Junkers but does not have concrete evidence.
Edit: Thinking realistically, there would be little difference beween the KoS and Pirate encounters; the only difference would probably end up being a few lines of RP dialogue, as most pirates are unlikely to drop stolen goods or loot. The general pirates get the benefit of RP engagement; the KoS targets do not.
Edit 2: This form may be subject to some minor adjustments.
