Hello!
You're welcome, and I am glad it's working on the client-side, shouldn't take more for the server-side to work as well. So I guess you are not using much caching or any CDN, right?
The .htaccess is written using the WordPress API in the function called "wr2x_generate_rewrite_rules" ("wr2x_settings.php").
The .htaccess line is something like:
RewriteRule .(?:jpe?g|gif|png|bmp)$ wp-content/plugins/wp-retina-2x/wr2x_retinaimages.php [L]
Maybe you can try something with that?
By the way, WP is NOT adding any rewrite rules if you don't use the Permalinks.