The government flip flopping on what is and isn't safe based on what they feel is important means any claim that shuls should be shut down because the government said so is moot.
Depends on the context. If someone says that it must not be safe because the government said so, you're right. If someone says we need to comply with government orders for other reasons, such as funding, aivah, relationships, or chillul Hashem, then the government is relevant again. I'm not saying any of those arguments hold water. I'm saying that just because the government is unreliable when it comes to science or math, doesn't mean they are irrelevant in other facets of our lives. I don't think anyone made the argument that shuls must not be safe because the government said so. If they did, quote them and I'll stand corrected.