Putting these in
httpd.conf (in your virtual host section for the repositories) is certainly possible. Additionally, if you are including the virtual host by reference to another configuration file, you should put the mod_rewrite directives in there.
I actually find it preferable to do this;
.htaccess files should be disabled whenever possible. This is particularly true on sites to which users can upload content, to minimize security exposure and keep configuration completely out of band. It also has performance implications -- the
.htaccess file is reread every time a URL to which it might apply is accessed, because it can change without a configuration reload, whereas the actual server configuration is only reevaluated when rehashing or starting apache.