I am just concern about security matters that will produce if I will give the user full access on .htaccess (AllowOverride All) on their webroot?
AllowOverride All effectively allows a user who can create a .htaccess file to access any file the Web server can read, and execute any code they would like to as the Web server user. From a security perspective it's equivalent to giving the user a shell as the Web server user. That may or may not be consistent with your security objectives.
Hope this helps!
-----Scott.