We had so many problems with subclipse under linux that we finally went back to the commandline! ...maybe it's worth giving it another try. But a few months ago subclipse with JNI was just a PITA.
Of course using JNI will result in more pain than a pure java library and if there was such a thing, I would not hesisate to use that one instead.
"Pure Java Subversion (SVN) Client Library" - http://www.tmate.org/svn/
JIRA uses this for its Subversion support. It has worked pretty well for us so far.
Cool ...you can hook it into subclipse!
http://www.tmate.org/svn/subclipse.html
And also IDEA is using it... Thanks for the pointer, mate!
cheers -- Torsten