Remove empty terms from array, sort alphabetically, update back to repeating field

$boat_safety_terms_cleaned_sorted = sort( $boat_safety_terms_cleaned );
error_log( print_r( $boat_safety_terms_cleaned_sorted, TRUE ) );

PHP’s sort accepts an array reference and sorts in-place, and returns success or failure – hence the 1 you’re getting. You want:

sort( $boat_safety_terms_cleaned );
error_log( print_r( $boat_safety_terms_cleaned, TRUE ) );

Also, I’m assuming I’ll want to use update_post_meta to save the array back to the field?

Yes, that would work fine. I assume this is utility method that you’ll manually trigger once per post though, and not something that gets run as a matter of course? If it’s on save of a boat then there are probably better ways to filter the value as you save it, depending on how you’re doing that.