If you are running this world on a multiplayer server, you can disable command blocks completely via the server properties. Shut down the server, open
server.properties with a text editor of your choice and set
enable-command-block = false
This disables all command blocks. Join the game, destroy the command block in question and reenable them afterwards.
In singleplayer, it's a bit more complicated. You have to open the world as a multiplayer* server. Open
server.properties and set
level-name = [relative path to your savegame]
/ to divide folders).
*If you haven't run a multiplayer server yet, you can download the server.jar (or server.exe) from the Minecraft website and save it wherever you want. Run it once to generate some files, including
server.properties and a savegame called
To join your own server, connect to
127.0.0.1 in Minecraft.