In teaching literature, and presenting a "Christ-like" character without offending anyone, I always recognized that different people had different beliefs. However, I noted that I was not sharing my opinions, but presenting information with facts from a story (like Kafka's The Metamorphosis) to support my assertion. Students are always allowed to believe what they wish.
In teaching Darwin and evolution, I would (in this case) present the topic as Darwin's theories and facts; we present what we know, along with what we think.
I would also inform the students that it is an educational exercise, not a lesson to teach these philosophies or theories as things they must accept. We give students the opportunity to study what we do know, coupled with what we think we know—the rest is really up to the student. Giving them choice is important.
In that Darwin's studies removed "God" from the equation in nature, I can understand that people would be uncomfortable with accepting what he had to say. (Personally, I'd be one of them.) But again, we choose what we want to believe: in God or in the absence of God; or that Gregor in Kafka's tale was a large bug or just the symbolic representation of a man who felt alienated from society.
It is important that a student have the ability to recognize the presence of others' beliefs in the world around them, even if those beliefs are not their own. In this way, we promote tolerance for the views of others that may be different. And we educate students about the world in which they live. Knowledge is power.