Sorry to hear you don't like them - I use them constantly to avoid opening another editor.
I'm not sure if we can disable them "globally" in a generic fashion but we could look into it, at least only for files we know. Could you please open a feature request for this on https://jira.jboss.org/jira/browse/JBIDE ?
btw. the way to distinguish folders from files in eclipse is by the folder icon - not the file.
...and how come you survived with having Eclipse JDT installed, it does the same for .java files :)