Is there a way to generate a Javadoc directly from an SVN repository? (or do I need to actually check out the code?)
You can do a svn export
to a temporary directory, generate the javadoc, then delete the temporary directory. Do this in a script. Then it feels like you did it directly.
The idea is to never interfere with the repository. Thats why you have to create a working copy to make any modifications. If you use continuous integration tools like Continuum then you can have JavaDocs generated automatically for you. I think (correct me if I'm wrong) that the continuous integration servers check out your code and perform these taks for you so you do not have to perform them yourself.
If the Subversion repository is accessible via HTTP, then you might be able to mount it as a WebDAV filesystem, depending on OS support...
but really, it's simpler to just export the sources, run Javadoc, then delete the export as Dave suggests. If you're going to be running Javadoc multiple times then check out the sources once and just update before every run (to save time).