In the case of Homeward it was just there to separate who among the many faces of the galaxy the Federation can help out. It's an arbitrary notion that warp drive should be the litmus test but it's there.
Before we get too high and mighty, how many genocides have we let happen since WWII? And hell we let known terrorist Gaddafi rule Libya because he kept the oil flowing. We keep monarchists quelling democratic uprisings in Saudi Arabia because we get oil and have bases there.