"I'm glad to hear that you've chosen to take action."
He tries not to show how worried he is about the kind of action that the Grand Theologin has chosen. "War of the churches"? War between citizens of the Empire is something Rudiger would very much like to avoid (if possible).
"I hope we didn't unwittingly offended the Lady with our behavior. "
"... because when I offend people, I like to do it deliberately.", he finishes the sentence in his mind. Her behavior certainly offended him by reminding him of his arrogant half-brother. Arrogant and treacherous, he to be more precise. And what if...
"And I hope she won't be even more offended once she realizes that the money she gives to the church sometimes has to pay for things as unpleasant as this w... disagreement between the churches."