PHP provides the function number_format to format numbers with decimal points and thousands separator. Actually, if there was a way, in Drupal, to customize this function at site/user levels... :-)
I believe this is not so difficult to implement. All we needs is add a couple of fields to allow admins/users customize these options (decpoint/thsndsep) to admin/settings and user/edit, maybe near the date format?
Does it worth to roll a patch for 4.7?