Even without toggling on Non-Lethal Attacks, the Mother Superior can be knocked out. However, you must toggle on Non-Lethal Attacks to actually trigger the correct dialogue afterwards, or she will speak as normal. Still bugged as of 4.1.1.4251417, but patched at least by 4.1.1.5022896.
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https://www.youtube.com/watch?v=fAzJszg0aUA