The option sonar.phpcpd.shouldRun allows user to disable phpcpd execution.
Moreover, there is another useless option named sonar.php.cpd.skip that does the same job.
A standard sonar option named sonar.cpd.skip already exists, and it should nice if phpcpd is disabled if this option is also set.
The rule could be:
if one of the options says disable it, phpcpd must be disabled.