If you’re not going to use those plugins, have at it. No reason to keep them around. Direct SQL query should be fine.
Related: add_post_meta() has a nifty argument to prevent this very problem. The fourth argument is a boolean, declaring whether the meta should be singular:
add_post_meta( $post->ID, 'my_foo_bar', 'value', true );
Source: Add Post Meta | WP Codex