WordPress.org

I use jQuery but the plugin outputting its own JavaScript

You may not be loading your JavaScript the WordPress way. If wp_enqueue_script means nothing to you, then have a read of a tutorial I wrote on the subject

My stylesheets aren't been loaded any differently

Make sure you are using wp_enqueue_style to load your CSS, an explanation is in the Installation section of this readme file.

Can I use IE conditional comments

Yes. If you set your stylesheet to be for a particular version of IE, this plugin will respect that.

Is this plugin safe to use on a production site?

This plugin was written as a proof of concept, has a sub 1.0 version number and has been tested for a few common situations only. I don't use it on a production website but let me know of your experiences if you choose to.