Yes, I can see that interfering with the paper is not good.
'They have harmed the education of their pupils by interfering with the exam - apart from anything else, their students were prevented from answering those questions, and will have been marked down.'
But my guess is that they may never have taught that aspect of the syllabus anyway, if they went to the lengths of covering up questions about it.
'They may disagree with the theory of evolution but they have no right to pretend it does not exist as a concept.'
My guess is that they tell their pupils that it exists as a concept, but just don't go into detail teaching it because they think it is wrong.
If they have very strong views about it, I don't think they should be forced to teach what goes against their core beliefs, since that would undermine their beliefs and way of life.
It is not an issue that bother most of us, but if they feel that strongly about it, I think they should be allowed to leave that part of the syllabus out.
I think that some flexibility and respect for their core beliefs and way of life is better than forcing them to go against what they hold dearly.