Don't worry about your teacher's reference "outing" your views on abortion and hurting your Boston University admission odds. Even the most liberal institutions value--and encourage--a range of perspectives, and I promise you that if you aren't admitted to BU, it will NOT be because your abortion stance is more conservative than the prevalent opinion on campus.
What does concern me, however, is that you seem to be talking about submitting the recommendation yourself. Instead, you should request that your teacher's letter of reference go directly to the college from him--or from your school--assuming that it is one of your REQUIRED teacher recommendations. (If it's an extra, optional reference, it can come right from you.) Colleges prefer to see references that were written confidentially and to which students do not have access.
Admittedly, there seems to be a growing trend among teachers to show their letters to the applicants involved and sometimes to even ask for feedback (e.g., "Is this what you want me to say? How should I change it?"). However, admission committees take good references more seriously if they don't appear to have passed through the candidates' hands first before arriving in their offices.
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