Uh I think, you straight up missing the point of the
@Boohoo the 3rd post. It don't even have anything to do about GUN at all.
If anything it shows that revenge is pointless and is always hurt more people in the end thus continuing the cycle of hatred, Eggman if anything is move by a grudge against GUN.
What you don't expect destroyng GUN also have no consequences?
Oh no, I'm fully aware of it. In all honesty, do you think Eggman would be any more merciful towards GUN or less. But no, my point is that once you commit to rulership, you have to consider more than just your own fate. Mercy is a choice with consequences, much like revenge.
Whisper's decision will leave someone to pick up the pieces, and there would at best w very limited supplies of mercy for those under Eggman regardless of who eventually sorts it out. The Restoration at best lasts a decade after Eggman dies, with GUN being the likely ones it will fall to sorting things out.
The fact of the matter is, GUN has every reason to beware our accumulation of power. Especially as we're dipping into fields Eggman never explored in the main canon.
Trust, Loyalty and Teamwork are things that he never really dealt with before. Usually it was just him, Metal Sonic and thousands of utterly expendable badniks. Now we have subordinates, valuable ones. Ones that we, as players, care about. While certain groups are trustworthy, we also have to consider what would happen if by helping them they get kidnapped.
The good news is that due to their variety of natures nobody has the means to mind control all of them at once. Psionic methods will not effect our mechanical servants, while hacking won't affect organics. If we could get aboard some spiritual allies, such as a genie like Shahra or a poltergeist like Filch, we'd have even more options.