Yes, cut & paste to Word/notepad may lose fonts, etc.
Another thought, if the message in HTML format then each GroupWise message has the TEXT.htm file which store the HTML contents of the message. It could be possible to save the TEXT.htm file, render contents (i.e. remove disclaimer, etc) then open the TEXT.htm in a browser (i.e. Internet Explorer) then print. Also depend on whether disclaimer/meta data you want to skip from print, easy to identify (i.e. in a specific format).
As I said earlier, all these workaround will require significant changes to the applet. If you have in-house Visual Basic Scripting (VBS) programming experience then you can use the Formativ to modify the applet. Otherwise you need to contact our partners (http://advansyscorp.com/resellers_formativ.htm) for custom enhancement.