To allow MCM to overwrite existing files you need to edit this file:
downloader\lib\Mage\Connect\Validator.php
and remove this part:
if (file_exists($dest)) {
$this->addError("'{$file}' already exists");
return false;
} which is right at the bottom of the file
If installation fails you will need to re-edit the file as it will be replaced by the version just downloaded