Aegis are pretty much INRA reborn, there is more than enough evidence to support that.
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In what way?
Same as in "science and defense organization founded by superpowers as an answer to the Thargoids that the founding superpowers considered a threat"?
Or same as in "doing things outside of their direct mandate, killing other humans to keep things secret and overall doing things considered amoral in most human societies"?
If it's the later, then evidence is a bit sparse - unless you consider one "evidence" that could equally be just the result of the BGS having a hiccup to be enough.
Sure, Aegis is doing military research (defense and weapons), they consider the Thargoids hostile, the don't share every information they have with everybody.
Beside that, there is only that "black flight" DBXs at that installation that previously hadn't a faction identification and now have the faction identification of the controlling faction of that system.
But even if that "black flight" organization is indeed Aegis. How does that turn Aegis into an evil organization?
In case of that installation they just protect their territory. They don't attack if you don't get to close. They don't attack unless provoked. (btw, does anybody notice a similarity between the behavior of those "black flight" DBXs and Thargoids?

) And if I remember correctly they even warn trespassers that they will attack.
That they tried to prevent other humans to provoke Thargoids by doing "research"? We all know what happened after CMDRs encountered Thargoids - the first thing they did was shooting at them.
How far would you have gone to prevent other humans to provoke Thargoids and/or attack Thargoids?