Sorry I'm late on this one...
That's how I do it. The problem is that some web hosts out there hide features like SSH from their customers, so the only way to do it is to upload each file individually. I had to do a vB upgrade for a client on another host a couple of years ago, and they had no SSH on their server. I started the upload and took a long lunch break.
I upload, unpack, change to the /upload directory, and cp -pR /to/my/forum/directory . It actually takes longer for XF to upgrade the templates and phrases than it does for me to upload/unpack/copy.