Sure it can.
Just like you could call Wankerpool a crappy team because that's what they are today, whithout being affected by the throphies they won back in the days of horrible haircuts and facial hair. Yet they are still a continuation of the team that started playing in Liverpool over a hundred years ago.
I don't really see why acknowledging the horrible crimes committed by guys wearing the pointy hats way back yesterday should affect their link to the very beginnings of the church. They could just see it as a longer version of this: good times -> some rotten years -> good times again.
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