History and website data are two different things. If privacy is very important, you may indeed need to clear both. But for everyday usage, just clearing history is usually enough. The problem with clearing website data is that you have to relog into every website, every time (i.e. the "remain logged in" options are reset) after a clear.
In the past, we could clear both independently, but now the quick way clears both. I can always open the history pane and manually select them all and erase them. But it's a bother compared to what it used to be.
I wonder if there's a plist we could change to revert to the previous behaviour? I'll try and take a look.