I could see dropping the case if it had been a medically necessary abortion instead of an elective abortion. But under our system of government, the way to get rid of the Church Amendments is to get Congress to change the law, not for the executive branch to stop enforcing the law.
Yes and no. As you well know there are scarce resources in all areas of criminal justice: policing, prosecution, the courts...
Those who are in charge always have to pick and choose what areas to concentrate on. This is very much the same as the Los Angeles County Sheriff who refused to go after people for not wearing masks even though the Los Angeles County government brought bask the mask mandate.
However, if religious exemptions are going to be concentrated on as an area of enforcement, I hope that thousands of medical professionals join a religion that argues that people who don't get vaccinated should be left to themselves, and refuse to treat unvaccinated people.