You might ask how the President can change state orders.

Most state orders import the federal "essential / non-essential" list that does, in fact, originate with a Presidential Policy Directive. (PPD-21). https://twitter.com/nprpolitics/status/1263891875989159944
I imagine the administration will amend PPD-21 to state that Churches should be accommodated by the same rules, given the constitutional protections of religious worship.
States will then have to prove their own exclusion of churches meets strict scrutiny. But most of their "essential" lists already allow far bigger gatherings than most churches.
Which then gets turned into the "essential" list at the Cyber Security and Infrastructure Security Agency (CISA): https://www.cisa.gov/identifying-critical-infrastructure-during-covid-19
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