You can make flawed societies sympathetic. In fact, you pretty much have to, unless you're writing about a utopia or writing an anarchist manifesto.
In many fantasy and historical stories, the good side has public executions and mutilations, torture, slavery, etc. And yet, we're able to see them as the good side. Sometimes, the other side is more evil; other times, there's an Evil Grand Vizier who's worse than the society as a whole. Meanwhile, we meet dozens of people who help our heroes, who are brave and kind, and painted as sympathetic even though they don't know anything better than the society they grew up in. Maybe you'll have a scene where one of the wiser good guys laments that they can't end slavery because stopping the Evil High Priest is too important to focus on a quixotic crusade to overturn a fundamental institution of their culture.
In fact, you can see all of that in the Star Wars movies—not to mention the Ewoks, who kill and eat other sentient beings—and yet nobody comes out of those movies saying, "What was the point of all that when the good guys are evil too?"
For a more directly relevant example, see the 1964 Doctor Who story The Aztecs. Aztec society is painted as in many ways better than European society at the time (and one of the Doctor's companions, Barbara, directly points this out in case you miss it), with human sacrifice as the one thing that makes it worse. Most of the good guys (not counting our outsider heroes) continue to believe the religion they grew up with, but don't come across any less sympathetic. The one exception, we're pointedly told that he's not going to succeed in changing his society, and see him as a tragic hero.