Avoid the preprocess/hook function defined from the Zen theme is called for its sub-theme We are using a theme that inherits from the Zen theme. the Zen theme implements zen_process_html_tag() and zen_html_head_alter(), and we want these functions not to be called; we tried to override these functions in our theme, but then Drupal call zen's functions first, then the functions in our theme.

How can I avoid this happens?
Those are part of HTML5 support bundled with Zen 7.x-5.x. Your options are either downgrading to Zen 7.x-3.x or patching Zen. Please open an issue at Zen's issue queue asking to provide an option to turn on or off the header manipulation.