"or if some things that the Pope has to say and do on the basis of his conscience or the conscience of the Church seem hard to understand.""
This is an unusually open statement, I assume it refers to the fact he is now a politician/statesman in his role and will be required to say things inconsistent with his personal views or things he has done or said in the past, as his obligations have changed dramatically.
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That might be what he meant by that statement. I took it to mean that he was telling them that they should not turn away from the church or from him if they personally disagree with some specific position held by him or by the church.
yeah, it is hard to tell given the lack of quoted context in the article.