One of the random events is a bit funny about this. But ultimately in short, you are attacked by the Zoltan, you fight them off, and then the ship hails a cease fire, as it turns out, its captain was testing you, to see if a diverse crew could work together and protect your ship, and since you just did, he joins you.
Letting KazaaakplethKilik participate in and destroying the Rebel Flagship could be this in a way. You saved his life and redeemed him from thievery to become a legendary hero of the Federation.
One event involves coming across an engi ship under attack by rebels. After you save it you note that is poorly equipped for outrunning the rebels the sector. If you donate the maximum amount of scrap along with other military supplies to the Engi the sheer generosity involved in saving them twice causes them to be so overwhelmed they generate error messages, a clear equivalent of tears of joy. "Generosity magnitude unpredicted. Well-being syntax error [value too high]. Accept this token." Said token is the Engi medi-bot dispersal augment.
The "No Redshirts Here" achievement. It requires you to beat the game without any crew member dying. Overlaps with CMOA.