I'm assuming Sister Sage has her own agenda and is using Homelander. Or she cares more about supes over caring about racism. Also the tool that sister sage used was probably a lobotomy tool. Probably makes her temporarily "high" as she regenerates/heals
I think she uses it to temporarily make herself dumber so that she can enjoy more low-brow pleasures like Bloomin' Onions and Transformers 2. Also lets the audience know that she has abilities beyond her super intelligence--Butcher and Co. aren't aware and will doubtless find out the hard way when they try to take her out.
