I believe an actual Omega order was issued on another minor (A, maaaaaybe AA) corporation. The 'Theta Order' is the Ensenada strike, and it was more along the lines of the corporate court giving Aztechnology a 'warning shot across the bow': "Play nice or we'll wax you like a brand new Lamborghini." As Danchekker showed, however, taking out a major megacorporation (he was after Novatech, but any of the other Big 10 are applicable) was less a matter of doing it completely on your own than it is prying apart your economic structure - and once blood is in the water, the rest of the sharks come a-feeding.
This means that in at least 80% of the cases, the corporations and facilities that make up Aztechnology simply won't have AZT on the door or in the ledger books any more - they'll have S-K, or ARES, or EVO, or MCT, or Yakashima, or any of a couple hundred different corporations that would quite willingly take a bite out of the AZT, or snap up any scraps floating in the water.
For the sake of clarity, however, in regards to the other examples offered:
Fuchi / Novatech / NeoNET: JRJ International was never 'picked up' - it was a quiet internal transfer by the primary (and, technically, constant) owner, Richard Villiers, from Fuchi Americas to Novatech. That transfer, when Villiers made Novatech public, allowed Villiers to a) swipe a corporate court member from Fuchi (as one is permanently assigned to JRJ-or-its-parent-corporation) and therefore b) become a AAA megacorp by default. When Novatech pulled the IPO and wound up merging with Erika and Transys Neuronet, the new corporation (NeoNET, literally 'New Novatech-Erika-Transys') became the parent - though you can bet your toes that Villiers remains the overwhelming shareholder of JRJ International.
BMW --> Saeder-Krupp, ORO --> Aztechnology, Yamatetsu --> EVO: naming conventions, though only the first two are permanent, non-disenfranchiseable members. Keruba got bought out by Renraku (I may be wrong on this, since for this moment I'm relying on the Wiki, which clearly hasn't been thoroughly updated in years), which means Renraku is theoretically in the same position as NeoNET - Keruba being theoretically vulnerable to being bought out from underneath them, though I somehow also remember this as being incorrect; Keruba --> Renraku was, I thought, just a name change, but like I said, I could be wrong.
As for White-Hat Aztechnology, well, here's the thing: if given the devil as proven (AZT being 'shown as being the devil'), if you figure that people are going to shrug their shoulders at that, they're going to do the same thing on AZT's big reveal to prove they aren't bad guys - which is to say, 'yeah, right, whatever'. And in truth, it's exactly that which would backfire on them - because they're making weapons against bad things that they claim are going to come across in two hundred or five hundred or a thousand years, at the earliest. People will say, 'Oh, yeah, right, pull the other one. Here, have a bullet to the head.' Basically, you can't have it both ways.
And since there's no evidence, either with the IC fluff, the OOC fluff, or the crunch, that Aztechnology is doing what the 'White Hat Aztechnology' theory suggests, and in fact every single piece of evidence is a full and direct indicator of the opposite - that the PTB at the AZT are in fact trying to suck up to the super-nasty-bads in order to be 'off the menu' - it really kinda looks like the WHAZT theory has nothin' but hot air and sweet rainbow-farting unicorn wishes behind it. :/ Sorry. Remember - 'out-of-game-world' means there isn't an 'unreliable narrator' issue; facts is facts.