Wow this is an old thread -
Well, I was having the same issue - here's the vanilla fix - no plugins:
This is assuming you have daily backups and access to Minecraft 'world' directory via FTP on the hosted site.
Logout of Minecraft and stop the server.
Login to the FTP and backup the current 'broken world' to your local drive.
Make sure you have a backup of your world, if so, delete the one on the FTP and copy a day old backup of your world from your local drive or the server side to the FTP.
Start the server, login to Minecraft and go to the location of where the offending looping command block would be on the 'broken world', and write down the x y z, x y z location (Press F3 for info).
Stop the server, login to the FTP and delete the day old backup 'world' file.
Copy the 'broken world' file from your local drive to the FTP.
Start the server, login to Minecraft.
Type this op command:
/fill location of command block minecraft:air
/fill 19 53 351 26 54 350 minecraft:air
If that works, save it.
Hope that helps,