How to withdraw a published paper when former boss seems to be raising ethical and data integrity issues with the editor?
The publisher is unlikely to let you withdraw the paper unless you convince them there is an extremely serious problem with it (misconduct or an unfixable mistake).  They have an ethical obligation to make the paper available to the research community, regardless of whether you regret publishing it, and it takes a powerful argument to overcome that obligation.

In particular, if you ask to withdraw the paper, then the publisher will assume that the accusations against you are true.  If you succeed in withdrawing it, then the entire community will assume there was something terribly wrong with the paper (and, if you don't publicly identify errors in the paper, they will assume it was an ethical problem).

In other words, withdrawing the paper is tantamount to admitting guilt.


  I have at least a dozen of emails attesting he knew the study, but I don't know if I can show them to publisher.


Yes, you should certainly make use of any evidence you have that the accusations are not correct.

There should be no problem with the ethics statements.  Presumably you have proof of approval by the appropriate review boards (or, in the worse case scenario, they can confirm their approval).  If you don't have proof, then maybe there really is a problem.

As for the other accusations, hopefully the e-mails from your former boss will help clarify the situation for the editor.