Babylon may have "good" intentions but we see that the Church does too hoping for them to improve the situation while Babylon wants to provide them with "order" to keep them in their spot.
It's a tough situation in either case.
The Church is prepared to gamble the situation where- should it succeed in radical change, it'll still leave bad blood between the normal citizens and the refugees if it's a violent uprising with a lot of bloodshed. Their treatment will get better officially, but without some seriously good PR or a short and low-casualty war, bad relations will stew.
That's assuming success. If they fail, they kneecap any chance of Babylon's plan being a fallback and may result in the Refugees getting way worse treatment.
Babylon's way of doing things will be a gradual upwards incline, keeping law and order in the area. Along with 'accidents' hitting the ones opposed to improving their living condiditons, which they don't seem to be doing a huge amount of those. In any case, it'll be slow and may take at the optimistic
least a Generation or Two to really make a difference at first to improve relations with the citizenry and country itself. That's assuming the assassinations aren't revealed as assassinations either. Then it'll still take a long time for Refugees to reach a very good standard of living. Slow and ineffectual, to be expected of anything that requires any amount of Government agency and societal shift.
Basically, fast and dirty or slow and steady approaches are the choices here.