It's possible that the worker revolts on Ardana are simply a very recent event, and that all was well and good when they joined the Federation.:
The dialogue would suggest the caste system--and grievances about it have lasted for some time:
VANNA: To welcome our honoured guests as I was taught to do when I served in your father's household.
Vanna's statement could not be read to mean she recently served in Plasus' home, since she holds a position of authority among the Troglytes, which did not happen overnight. Her every word strongly suggests she--and her people--have been in turmoil about the system for some time, and if that's the case, the Federation would have been aware of Ardana's culture and business practices, too. Again, no government just walks into agreements not knowing a thing about the partner.
Then, there's Droxine's exchange with Kirk & Spock:
DROXINE: The complete separation of toil and leisure has given Ardana this perfectly balanced social system, Captain. Why should we change it?
SPOCK: The surface of the planet is almost unendurable. To restrict a segment of the population to such hardship is unthinkable in an evolved culture.
DROXINE: The surface is marred by violence, like the Troglytes. But here in Stratos, we have completely eliminated violence.
Droxine is not talking about her world's practices and Troglyte perceptions as if it a series of recent events. She speaks of the surface--and the worker Troglytes as being violent. In the minds of Droxine and her people, that is the way the Troglytes have always lived, and one cannot believe such turmoil--including anger and revolt against their "masters" in Stratos were just erupting shortly before the arrival of the 1701.
...except that
Ardana has a sole "ruler."
This ruler has the legal right to have criminals executed if their crime warrants it.
...and that's how harsh the Ardana government is--a government the Federation was not in the dark about, but its Starfleet couriers (as its not their job or need to know) were.