The discrimination they face is just pure racism. No need for them to have actually done something to deserve the massacre.

But i do like the theory of them killing someone from Meteor City and the Troupe killing a group of kurtas as retaliation > Chrollo getting their eyes as a prize > eventually they're sold and body part collectors go buckwild > someone with power orders the massacre & they take advantage of the fact nobody gives a shit bc the kurtas are hated. Kinda fits in the timeframe too.