I don't believe in forced eugenics at all, it should be optional. The snag that hits is one of the reasons I mentioned Gattaca, the regular people will probably end up becoming de facto second class citizens to improved humans.

How do we stop harmless mutations from being labelled as “defects” to be purged?

That is a big problem, I mean it's not just minor stuff that seems harmless. Tendencies towards things like drug addiction and violence, or mental illness, are negative traits that seem like they should be attempted to be bred out if possible, but you'd be erasing a lot of important people in history were this, just as a thought experiment, able to be applied retroactively.

We'd need to reassess what traits are truly undesirable, honestly, and we probably aren't going to be super happy with the results.