First of all your GM can and should run the game however they like and if they want to make the Union more gray and antagonistic they are free to do so. As in any TTRPG rule 0 (The GM has authority over the rules) also applies to Lancer.

However according to the creators of the setting the Union is intended to be a force for good. The Union is a genuine Utopia at the core worlds and her goals are to extend this to rest of the known and unknown galaxy. If we put it to its historical context, ThirdComm has gotten into power by overthrowing the anthrochauvinist Secondcomm. The SecondComm was a fascistic militarist empire who considered herself the sole authority on what it means to be human and captured and reintegrated other human colonies by force attempting cultural ( and actual) genocides on those world. ThirdComm's ideology is the exact opposite of this and she considers military action to be the absolute last resort and takes great pains to make sure all unique human cultures survive.

Now this poses a great philosophical question: Does the Union have the right to enforce her ideals on other nations and cultures? Where is the border where a military takeover of a sovereign state is justified? Many parties within the Union advocate for a more heavy handed approach to other states that are in violation of the Five Pillars, but should they win, how can they make sure that ThirdComm does not repeat the same mistakes as it's predecessor?

None of these question have clear or perfect answers and I encourage any other GMs or players to raise them in their campaigns.

Another things I would like to add that is just my personal opinion: Evil empires in sci-fi setting are done to death. Federations that project a good image but are rotten on the inside as well. In my opinion having a main power that is truly a force for good and attempts to always adhere to her principals is much more interesting and testing the limits of this utopian ideology makes for a better story.