The thing that stuck in my craw is that I had to swear an oath that included the words "so help me god" as did all the witnesses.
I did that to get a federal job. I sort of wish I had voiced my concerns; but of course the advantage of atheism is that there's no metaphysical repercussions to feigning religious affiliation. It does stick in your craw a bit, though.
It's my understanding that folks like Jehovah's Witnesses, whose religious beliefs preclude the swearing of oaths, are allowed to affirm, etc. Probably you can choose to avail yourself of the same option?
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