I'm an attorney. No, the churches likely wouldn't win.
Think of fire codes that limit the number of people in a building. Those fire codes apply regardless of why people might assemble in a building, whether it's for what's widely regarded as highly protected speech (e.g. religious services, political party meetings, etc.) or assemblies that don't have the same type of First Amendment scrutiny (e.g. a concert or sporting event). As long as a fire code is neutral in its application (meaning that it's not *specifically* applying rules to religious institutions that are somehow more discriminatory than any other type of group), then that's going to pass constitutional muster because the government has a compelling interest in the protecting the safety of its citizens that overrides any First Amendment argument for that particular situation. As a result, a religious institution can't argue that the government is infringing upon its freedom to assemble because a fire code restricts the number of people in a church building to 100 people even though 200 people might want to attend a service.
In essence, the orders limiting the number of people gathering in one place that you're seeing across the country are the equivalent of a national fire code. As long as those orders are neutral in their application and not somehow more stringent toward religious groups, they're likely to be held up as constitutional. (To be sure, I certainly believe there will be groups that will attempt to sue on constitutional grounds just on principle, but I doubt they'd get past the motion for summary judgment stage for the reasons that I've stated above.)