The simplest way to stop the warnings is to set:
allow_call_time_pass_reference to TRUE in
your php.ini, but that's only a quick solution as you may have problems in future versions of PHP.
As noted in this sentence from the PHP docs:
"This method is deprecated in PHP 5.3.0 and is likely to be unsupported in future versions of PHP/Zend."
You can also change your error reporting level to quash the error notification.
Lastly; which is probably not the wisest as it might return if you upgrade phpMailer and they don't fix it the call in their code,
is to remove the ampersand preceding the passed arguments in errant the lines you've noted in your post.
(On the above, you might be: using an older version, the folks that put out phpMailer haven't modified the code or you're using the php4 version.)
RE: changing the code...
This error won't keep the module from running.
As far as the version goes, just choose close to latest stable version for your version of PHP.
I can imagine it's pretty confusing since they have so many versions on SourceForge.
Hope that helps...