Check the Java -Dfile.encoding flag options (to be set in knime.ini), there's some flexibility in there. My own default is -Dfile.encoding=UTF-8, but I suppose you can pick any other from here:
One interim solution would be to create an R Snippet template that allows you to set the appropriate value for the 'eol' option of write.table(). (you can also set quoting, row/col names, etc.)