The files you upload at Savannah needs to be created / editable using free software, and the free replacements need to be at least as good as the proprietary one.
In the case of Gnash, it's currently not fast enough. Until the Cairo backend is done, it essentially requires a 3D card, which nowadays almost always run with proprietary software only; this is a non-trivial issue.
If your particular Flash file plays as well with Gnash than with Macromedia/Adobe Flash, there's no problem with uploading it at Savannah. In the opposite case, you're essentially enticing users to use Adobe Flash for a decent "user experience", so that's not a good value to promote.