I'm pretty sure that if it is someone making an Establishment Clause claim they wouldn't have to actually be in the program to have standing. So it wouldn't have to be an atheist facing the choice to get out or make waves and not get out while doing so. It could just be any random person within the jurisdiction.
(A legal blog I was reading about this at mentioned that in Mississippi a judge was recently suspended for a month for making bail contingent on church attendance.)
And apparently the ACLU
let it be known they have issues with it representing that random person and the program is on hold pending further review by the city's legal counsel (man, I really hope their legal counsel didn't previously tell them this was ok).
The sheriff's continued defense indicates he doesn't understand the problem it creates at all. Though this article makes it sound the program is just something he and the local judges came up with on their own.