I think perhaps you misunderstood what I was saying. Shadowrun is not like DnD. There are no alignments. Nobody is "good" or "evil". They just do things. Those things can be the result of a variety of motivations that the actor believes to be for the greater good.
Because the game sets up corps with so much power like private armies and extra-territorial powers, it's inevitable there will be conflicts or interest. Of course corps will sometimes do things that align with your own interests, but the most powerful motivator for any entity is self-interest. The primary self-interest for any corporation in the real world or in game is profit. Things that are most profitable rarely are good for the general public, so take away oversight and lots of shady stuff is likely to happen. Smart companies will try to do very good things publicly in order to keep up public perception, so it's up to us as GMs to use that tool to make the world more real, but I think like any other NPC or PC, corps need motivations for their actions and what most folks would consider "good deeds" rarely align with the primary motive of profit.
Most of the "evil stuff" corps do in my stories are a direct means to and end. Need to get that new product out faster? Maybe accelerate human trials. Maybe those participants are willing, maybe they are unaware. Or maybe the Corp giving you a job got some intel that another Corp was doing these trials and hires you to disrupt. It's up to us not to fall into simple good v evil tropes.
I like how that sounds, but that really doesn't describe the vast bulk of cyberpunk-genre role-play over the last few decades, and believe me – I was there!
If anything, most of cyberpunk role-play has been even more behavior-tropic than D&D tends to be. The alignment system in D&D at least allows for characters to break the mold of expectation. A Chaotic Good goblin is at least theoretically comprehensible within the framework of narratives that tend to fall out of it. Unusual, yes. But allowable within the framework.
Approach most groups about how often their Johnson screws them over and you will get elaborate laughter, vast peals of it, and they might talk about the one or two instances in their entire gaming career where the corporate contact doesn't screw them over one way or another. Maybe. If you're lucky and they've been particularly lucky.
If you look at the published scenarios, all the way back to Cyberpunk 2020 but the vast corpus of the last five editions of Shadowrun as well, there are almost no examples of corporations which cannot easily be painted very broadly as "evil."
That trope is extremely widespread even outside of the specific context of cyberpunk RPGs. In fact, it's one of the main reasons that I pitched loudly and long enough to get handed the Iteration X Revised book for White Wolf just so I could get some corporate entities into RPG canon who weren't complete mustache-twiddling jackasses.
Which is exactly why I originally pointed out that it would be an excellent requirement for the players to get on board with their part of it by needing to justify, by buying into, and by explaining why the corporation that they are responsible for creating as antagonists are doing good things.
I would make that a part of every cyberpunk-genre game that I ever ran, but in particular for The Sprawl and the kind of lightweight distributed narrative power that comes in that system, that is a huge, potentially interesting aspect which actively pushes the players away from falling into the simple good versus evil tropes.
Which I repeat, are dull as dishwater.
Anything that breaks that cycle is a good thing.