The way I solved this was I had to modify the agent side plugin so that the plugin output could be generated for my 4 MYSQL instances running on the single server. I had one more problem : the mysqldadmin and mysql binary were not available as root user. It were available as the instance user.So, I had to modify this as well.
So, you can do few things to get this working:
If you have a Dev/Inte/QA server that you can try on that first
Create a copy of the original mk_mysql plugin in the plugins folder and then remove the execute permissions of the original plugin and then you need to debug the plugin. As I have no idea what is your Mysql setup? I won’t be able to tell you much.