Just another suggestion here... In a two-step approach, you could allow enabling/disabling plug-ins for future releases of plug-ins, making sure the developers add the necessary support in future updates. Then for existing plug-ins, have Mala warn the user that the current plug-in is not capable of enable/disable - maybe even offer them the choice to move it to a disabled folder for them (maybe requires a restart)?
In case I am not clear, here is what I am picturing... in the plug-ins section, there is a checkbox next to each plug-in. If I click on a supported plug-in, it simply disables it. If I click on an older version (hence not quick enable/disable supported) a dialog pops up telling me that this plug-in can't be disabled unless I restart Mala. If I choose to continue, it moves the plug-in to a disabled plug-ins folder, and on restart I see the plug-in without a check next to it.
I feel kinda if you have to quit mala then you might as well just drag and drop the plugin out of the folder.
For me, it seems if the software can handle it's own file/folder structure that is less work I need to do, and less that I need to know. Maybe akin to a program editing it's own configuration file vs. my needing to manually change a text file.
Just my opinion. Sorry if I'm not very coherent. I'm off to get my second cup now...