A quick glance at that plugin shows that it loads the filters from an option, trueedit_options. You might be able to add a filter to option_trueedit_options and check the context of when that option is being loaded and return an empty array. It runs on init though, so not sure how you’d determine that.
Another option is to add the filters back on in your header file. If you look in /wp-includes/default-filters.php you’ll see all of the filters that are added to the content which could potentially be removed by the plugin:
add_filter( 'the_content', 'wptexturize' );
add_filter( 'the_content', 'convert_smilies' );
add_filter( 'the_content', 'convert_chars' );
add_filter( 'the_content', 'wpautop' );
add_filter( 'the_content', 'shortcode_unautop' );
add_filter( 'the_content', 'prepend_attachment' );