Ban of Religion defined...

[Mr. Reactionary]

I believe OP is referring to church of the lukumi v. City of hileah. That case involved a local ordinance banning certain types of animal killings on the grounds that it was inhumane. It was passed soon after an event by the local santeria population at which several chickens were ritually sacrificed and their carcasses were later found discarded on the sidewalk. The ordinance exempted kosher and hallal food preparation  (undermining the argument that the inhumane treatment was the purpose of the law) but was still applied against the local santeria population. The supreme Court held that even though the ordinance was facially neutral, the surrounding circumstances and selective exemptions for some religions but not others demonstrated discriminatory intent. Discrimination against a specific religion triggers strict scrutiny which means the law is presumptively unconstitutional unless the government can overcome a very high threshold. I believe OPs argument is that banning immigration from countries with a very high population of one religious group is evidence of targeted discrimination in light of the fact that minority religious practioners may be exempt.

The tricky part about arguing this is that its foreign policy related. Zitolsky v kerry held that the president has a whole lot if discretion in how to conduct foreign policy and that some such decisions are political questions that cannot be decided by a court. The constitution does give the power to congress to regulate immigration. They have delegated some power to the president. If Trump frames the travel ban as related to the governments of the banned countries he might win. But presidential actions generally are still limited by the bill of rights. Its just a matter of when and where  you can sue. I haven't taken the time to see if this issue is carved out from the APA rules for when and how to sue over government acts.