As far as I know, it may usually (always?) be omitted. Oddly enough, it didn't require a Supreme Court decision, because the precedent was set with the first such oath: the Judiciary Act of 1789 was the first to specify a legal oath ending with "so help me God", and it at the same time explicitly included an opt-out clause, after which that has been accepted practice.

See Sec. 7 here: http://memory.loc.gov/cgi-bin/ampage?collId=llsl&fileName=00...

The fact that this accommodates atheists, however, is a bit of a coincidence: such opt-out clauses were initially included because Quakers objected to swearing oaths to God.