Jira doesn't ever update SVN. You can link it to SVN so that changesets can be linked to Jira issues but any kind of structural change in SVN would have to be done in SVN. Jira will just read changes & store them in a cache for display.
JIRA doesn't have such a function. To remove an SVN folder you need to do this straight through SVN command:
svn rm file:///path/to/your/SVN_REPO/foo/trunk -m "Removing trunk directory from foo"
You can also do this from a checked-out directory:
svn co http://myrepo/foo (or) svn co file:///path/to/my/repo/foo svn rm trunk svn commit -m "Removing the trunk dir from foo"
A bit late answer, but it maybe may help others...
This plug-in (which is a fork of the Atlassian's JIRA Subversion plug-in) allows to remove (and create, update, etc) artifacts on Subversion repositories from within JIRA:
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