The First Amendment prohibits government from promoting religion; it does not prohibit the government from taking steps to protect health and safety.The New Testament juxtaposes itself to the ritualism of the Old (as did the Lutheran and especially Zwinglian reform movements with regards to the Catholic Church), so compulsory actions along the lines of foot-washing have few parallels in contemporary American Christianity.
But the issue might conceivably arise. Say, hypothetically, head-rinsing in a university's drinking fountains led to demands for the construction of baptismal fonts at multiple locations on campus. Drinking from the same place that grimy college hair and face are washed is not a healthy practice. As is the case with the footbaths, secular people would be able to make use of the fonts as well. Would the ACLU, to avoid this problem brought on by an action entirely religious in nature, lend its verbal support for the fonts in the face of church-state criticism?
Some logic. Because a religious practice is unsanitary, special accomodations must be made to make it less so. Public resources must be used to ensure this. Taken to its logical conclusion, this argument may be employed in support of any religiously-influenced structure on public lands and/or with public funds that could conceivably serve up some health benefit, even if that benefit is realized in merely moving away from the rest of the general public the very believers who created the health concern in the first place.
The ACLU is not a defender of unfettered liberty. It opposes the Minutemen, essentially a neighborhood watch group operation at the national level. It supports mandatory, race-based quotas for public schools. It opposes the voluntary, transactional agreement between a private charity and drug-addicted women in the former compensating the latter for becoming sterilized (so much for pro-choice!). It is an advocate for the freedom of aggression against all that is related to the broad Western-white-middle class-bourgeroise social, cultural, and economic worldviews. There is scarcely a case the ACLU has taken up that does not make sense in light of this conceptual understanding of the organization's purpose.