For some stores, having paypal shown on the checkout pages is something that taints the user experience and can reduce conversions. I really doubt there's too many that this is the case, with most just crying foul without giving things proper investigation.
My advice - investigate things first. For those stores that really do need to remove it, the option should exist. The CSS method is the best, but until that is re-enabled on stores users are stuck in a holding pattern or needing to revert to crazy and totally non-recommend methods like below.
Before you check out this post I'd suggest you take a read of this earlier one, and the warnings it contains. What this posts talks about is a method that is far from official, and is likely not something anyone would recommend.
Also be aware that this doesn't discriminate on what it removes. If there's extra payment methods that are introduced later this code will probably remove those too.
This is pretty old post and the warnings talked about here are still totally valid. With that in mind there's a better way to make sure paypal doesn't show on the checkout step and that's to show it on the cart page instead. There's some insight how to do that in the Shopify docs.
If you don't want it on the cart page either, just use CSS to hide what you added via that link above. This does mean that you will need to push customers to the cart page instead of redirecting them from a quick cart / popup but it will remove any super crazy hacks you might still be willing to make. This is still hacky, but a far safer kind.