how to remove joint MD

Simply use section 284.

Pass ordinary resolution of shareholders u/s 284 in the general meeting and remove him/her from directorship. File form-32 within 30 days of removal in GM

Also check your articles in this behalf.

How to removal a director from the post of JMD and not from directorship?

no need to remove him as JMD. As per law MD must be a director so if you remove him as a director that would equal to removal as JMD....bcoz without directorship he can not continue as JMD.