During Garrus’s loyalty mission in Mass Effect 2, players will have to make a decision that will have certain side effects. Garrus wants to catch a teammate who betrayed him between Mass Effect and Mass Effect 2.
During the Eye for an Eye mission, players will help Garrus catch his quarry and will have to decide if they want Garrus to kill the target or not. This decision will have a major impact on Shepherd gaining Paragon or Renegade points, so it should be the main driving force of your choice. If you help kill Sidonis, you get Renegade points, while saving his life and you get Paragon points.
While Sidonis did betray Garrus and his team to Blue Sun mercenaries, if players choose to talk to Sidonis, they find out that Sidonis has been captured and forced to do so, instead of being something he wanted. He is also extremely guilty of what happened and will give up C-Sec if he is allowed to live.
While it really only depends on whether the players want Renegade or Paragon points, the main concern for most players will be Garrus’ loyalty. The good news is that it doesn’t matter which avenue you choose. Whether you kill Sidonis, help Garrus continue his own outlaw path, or free him and help Garrus turn in a more positive direction, he will still be faithful to you.