Override plugin option by with a custom theme

Plugin can read options on init event or just in code (during loading). All plugins are loaded before theme load. So, using init action can be too late.

Filter pre_option_fve_disable_css doesn’t change value of the option. Instead, you have to use option_fve_disable_css filter. But again, it can be also too late.

You should check the handle name in wp_enqueue_script function in plugin code, which enqueues relevant css and deregister this handle in your functions.php during wp_enqueue_script event. This is the right time for such an action.