While freedom of religion absolutely guarantees the right to refrain from choosing to submit to stem cell-based treatment, the same freedoms and the concept of separation of church and state absolutely preclude religious beliefs about when life "begins" (or about anything else) from dictating laws that affect other people who may not share those particular beliefs (Dershowitz, 2002). Beneficence and Non-malfeasance

Certainly, both the concept of beneficence and non-malfeasance absolutely prohibit the use of fetal stem cells from any fetus that is sufficiently developed to be considered a "person" as well as from any fetus that is sufficiently developed to sense pain. Medical authorities may debate where the exact point is where "personhood" first becomes an issue, but in principle, that characterization must be a function of objective criteria and never subjective beliefs of laypeople, especially based in religion...

Those duties would naturally require medical ethicists to err on the safe side and avoid ever exploiting a substantially developed fetus for research purposes (Levine, 2008). However, it is equally clear that a fertilized human zygote consisting of only a few undifferentiated cells cannot possibly be entitled to any "rights" since it is too undeveloped to have any ability to sense pain, much less to survive on its own.
References

Dershowitz, a. (2002). Shouting Fire: Civil Liberties in a Turbulent Age. New York:

Little Brown & Co.

Levine, C. (2008). Taking Sides: Clashing Views on Bioethical Issues. Dubuque, Iowa:

McGraw Hill.