Sure, you can do that (though this isn't in configuration yet -> I'll move it in). Here's how.

Crack open /core/members.php, find function show_registration() and the following section (line 445):

        if (strlen($data['member_username']) < 4)
        {            
            $errors[] = $lang['username_too_short'];
        }

And then do the needful. =) And the language string is under /languages/en/lang_members.php at #43.

I'll throw this into the config files for the next release; for now, just change the above.