The principle should be that you don't apply for jobs in which there is a reasonable prospect of a conflict with your conscience arising, unless you are prepared to override your conscience with good grace. Taking a job like that, then refusing to carry out a part of it for conscience reasons, is upsetting for those being refused service and is highly vexatious. You should resign or be sacked. If an unforeseen conflict arises once you're in post, I should think that sensible negotiation would be the way to go, within reason, but only for issues that most reasonable people would regard as issues. A greyish area.