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 however with most just crying foul without giving things proper investigation.
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.