I thought the AA "higher power" formulation left plenty of room for atheists who were more interested in recovery than in making an ideological point.
I'd take it more seriously if he were objecting on the grounds of effectiveness.
But assuming he's got a substance use problem that's impacting his work, then I figure it's incumbent on him to convince his employer that he's taking reasonable steps to treat it. It sounds like he did suggest alternatives, but they weren't within the scope of his employer's policy, so they were rejected.
I guess he's probably got a valid complaint here. His employer probably needs to reconsider their exclusive attitude towards AA-type programs.