is_a() has some valid use cases, so this would need to be done carefully.
is_a( 'class_name', 'another_class_name' ) is a valid use case and should be allowed.
is_a( $object, 'class_name' ) is not allowed and we should suggest using instanceof instead.
Unfortunately, auto-fixing here may not be very feasible, since is_a() may be combined with other checks like is_object() that would no longer be necessary. We may instead just need to report it back.