Cultural relations are still very much alive in the year 2183. Or, at least, that's the fictional prediction from the developers for Mass Effect: Legendary Edition. When fans think of the races in the Mass Effect trilogy, they'll think about humans, asari, geth, quarians, turians, and salarians. If they think of a few more they've had positive interactions with, they might even recall the volus and elcor.
Perhaps it is by design that the batarians are something of an afterthought. Even some of the paragon statements from Shepard put down batarians as little more than degenerate slavers. Of course, this is still no excuse for Ka'hairel Balak to attempt to eliminate an entire colony of people. When finally catching up with him on Asteroid X57 during the Bring Down The Sky mission, players will have a choice that has lasting repercussions until the end of the game.
Letting Balak Live
Nobody can say what the best choice is in terms of lore and story because everyone will have different preferences. But it should be noted that there are more perks associated with letting Balak live than there are with finishing Balak off.
Sometimes there are choices where players can have their cake and eat it too, but this isn't one of them. If Balak is allowed to live, he gets away and won't be seen again until much later. However, the hostages, including Kate Bowman, will survive.
Instead of battling it out with Balak, Shepard is given a short amount of time to diffuse three bombs while also attacking some more units that Balak unleashes while he escapes.
During Mass Effect 2, a news bulletin will talk about the failed efforts made toward bringing Balak to justice and Kate Bowman will send Shepard a thank-you note. Then in Mass Effect 3, Balak will get the drop on Shepard and have him at gunpoint. With some savvy persuasion, Shepard can convince Balak to join the effort against the Reapers, which will help in the war effort. Otherwise, Shepard can turn the tables and kill him without any reward instead.
Finishing Balak Off
Although it may result in fewer long-term rewards, killing Balak might seem like the right thing to do out of pure principle. Kate Bowman and the other scientists will die. The payoff, though is that, after a boss fight, Balak can be killed in a cutscene immediately afterward. He's got a few bodyguards and two varren, but it isn't harder than any of the other fights prior to this one.
Players may also choose to arrest Balak instead of killing him, which will give players a good mix of paragon and renegade points. This might be the best choice for gamers looking to max out both meters. Effectively, the game will proceed into future events as though Balak has been killed with this method.
Instead of the thank you-note, Shepard can learn of a ceremony for Kate Bowman hosted by her father Kate when watching the news in Mass Effect 2. Without Balak around, another batarian will step in and take command. This batarian will do exactly what Balak does in Mass Effect 3 and, like the previous choice, he can be negotiated with or killed.
This is a tough decision either way, even when knowing what the future ramifications will be. Hopefully, this helps clear the waters, at least a little bit.