Consider putting all your changes in a child theme. Look at my child theme as an example.

add to functions.php in your theme:

function dougbeal_unregister_categories() {
    register_taxonomy( 'category', array() );
}
add_action( 'init', 'dougbeal_unregister_categories' );
unregister_widget( 'WP_Widget_Categories' );

https://wordpress.stackexchange.com/questions/120418/completely-disable-categories
http://stackoverflow.com/questions/4249694/how-do-i-remove-a-taxonomy-from-wordpress