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Another question for the letter writer to ask is why continue in that college. Yes, finishing the degree is an important motivation, but by graduating from a school that has a reputation for a certain faith, carrying an implied endorsement of the student as a believer with a particular theology, will that follow the writer through a career?
I don't think the writer has any responsibility to come out as an atheist, but transferring (again) to a more amenable school is a big step in feeling more comfortable with one's own spiritual orientation. And I encourage continuing with freethinking and examining beliefs. There might be a time when it feels right to reveal atheism to others, and eventually to parents--it can take time, though.
And if there is some non-theistic religion and spirituality in your belief system, explore liberal religions such as Unitarian Universalism.