This is ultimately where I came out too. There was zero evidence that Sister Cathy had done anything to confront Maskell. In fact, she left the school entirely, which seems completely the opposite of what you would do if you wanted to protect the girls there. I keep going back to the quote from one of the other women who was in nun-training (I don't mean to be disrespectful, but I don't know the correct terminology) with Cathy and Russell, and she said they were both "very compliant nuns." I think it's entirely possible that even if Sister Cathy had some idea of what was happening, and even if she said comforting and sympathetic things to some of Maskell's victims, she didn't actually do anything about it. The same level of unquestioning obedience to priests that primed the girls to be victims would also have been operating in a nun who bought into that system enough to devote her life to it.
I think the series does incredible work in documenting the sex abuse and the church's cover-up. I think it is actually not very good at all as an investigation of the murder. Throughout, it doesn't construct any coherent narrative about who killed Sister Cathy. Its position certainly seems to be that she was killed by Maskell or someone acting with him, but it spends an entire episode digressing on two unrelated randoms, and up to the very end, it comes down pretty heavy on Koob as a possible suspect, which wouldn't fit at all with the Maskell theory. The more weight it gives any of those theories, it actually ends up undercutting the connection to Maskell.
It all comes down to two women, really. Sister Russell, who might have been able to shed some light on what, if anything, Cathy had done about Maskell, but did not. (And honestly, shame on her for going to her grave without telling someone what she knew.) And Jean, if she recovers further memories that link Maskell to Sister Cathy.