As of SFEE 4.3 SP1, you can do this using Velocity.
Create /usr/local/sourceforge/sourceforge_home/templates/body_footer.vm and populate it with this:
#set($superUser = ${PAGE_INFO.isSuperUser()})
#if($superUser == false)
<script>
if(document.getElementById("createProject") != null){
var e = document.getElementById("createProject").parentNode.parentNode;
while (e.firstchild) {
e.removeChild(e.firstChild);
}
}
</script>
#end
Save the file, and SFEE will start hiding the button for non-site admins immediately.