It’s said that this Bug is fixed in Subclipse 1.4. See http://article.gmane.org/gmane.comp.version-control.subversion.subclipse.user/12494 .
A workaround was to rename the containing project and the package (and perhaps the other packages in the project also), using the refactoring function of Eclipse for that. After that, deleting the package worked without problems.
Restarting Eclipse was no workaround.