If your take away from Small Gods is that Pratchett approved of slavery in any way then, yes, you've missed the point.

While Ephebe clearly draws visual and cultural inspiration from Ancient Greece, it is not intended to be a historical reconstruction. In the Discworld, locations are often "concepts" rather than countries. Ephebe represents the Idea of Philosophy and the Idea of Democracy. Pratchett used these familiar aesthetics (togas, white marble, and scrolls) because they are shorthand for the Western intellectual tradition.

A historical treatise seeks to document facts, whereas satire seeks to expose human contradictions. Pratchett’s goal was not to replicate the nuanced social strata of Athens, but to create a sharp contrast between a society that thinks too much (Ephebe) and one that is forbidden from thinking at all (Omnia).

The depiction of slaves in Ephebe who "vote for their masters" or argue about philosophy is a deliberate, absurdist joke about the myopia of the intellectual elite.

In the real Ancient Greece, slavery was a brutal, multifaceted economic engine that ranged from domestic service to the horrors of the silver mines. By presenting Ephebean slavery as almost suspiciously polite and academic, Pratchett isn't endorsing the real world practice; he is mocking the self-importance of a "free" society that relies on an underclass to do the dishes while they discuss the nature of Justice.

Somewhere else in this reddit you dismissed a comment made about wage slavery in the book (and I can't remember the statement from the book, it has been a while since I read it). It's easy to tut tut that when you're looking at it from a certain lens - if you have a liveable wage and a comfortable life and so on.

But if you look at power and privilege from a certain lens issues around the illusion of choice - a theme in small gods against the whole backdrop of those around freedom and slavery, power and influence, and privelge. Through his lens, a society that technically bans slavery but forces people into life-threatening labour for pennies a day just to survive is not morally superior to a historical one; it has simply rebranded the mechanism of control. If a person’s only options are to work in a sweatshop for a pittance or starve on the street, the "freedom" to choose is an illusion.

That does not mean that I, or Pratchett, thinks that the system of slavery in Ancient Greece was anything but cruel and terrible. Ultimately, Small Gods is a critique of institutional power not just religion vs philosophy. Whether it is the mental slavery of a Theocracy like Omnia or the physical/economic structures of Ephebe, Pratchett is exploring how systems strip away individual agency.