From my point of view E-Mails is a common used communication channel. It's generally considered as secure which might be true if everyone will set things right up like using SSL/TLS connections for POP3/IMAP or SMTP. In reality not all people know what these techniques are good for and just move forward with no transport security and so the misconfigure their system. So how to overcome this problem?

I would say there will be a safer way to provide an account to your customer. Think about your phone. No need to set it up and it works. So there won't be the problem of misconfiguration. So let's think about it a bit. I know SMS Token and calls are also not that safe, but it's a bit harder to get a SMS from another telephone redirected to the hackers phone. So why not using the phone number to send them a one time password which they use on a setup page and finish their registration? I would say this will be more secure then using e-mails.