I agree little chance the courts will reject vax mandates for the military. The courts have always given a great deal of discretion to military leadership.
WRT the religious argument for waiver, legally, the suggestion that previous vaccinations disqualifies one for making a religious appeal is not supported. What matters is what you believe NOW. People can change their minds. In this context one could say have an epiphany or revelation on the subject. ? Others might claim their view evolved. Admittedly, someone can be doubted for their convenient change in religious conviction, but the law would support it. Oh course, the military's religious accommodation is unique.