you need to deactivate that user : https://answers.atlassian.com/questions/127643/how-to-deactivate-a-user-programmatically-java-rest-sql
JIRA run whitin a java jvm .. this hardly mix with php.
if you want to use php , then you just have to call the jira rest api from your php code. you can easily do some rapide prototyping with curl or any tools of choices for rest :
if you dont want to make 2 disctinct call , you can create a REST Service Plugin with the above mentioned code , and then call this url from you php code .
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