Change whether file is executable
The relevant NSFileManager call, in Foundation, is - setAttributes:ofItemAtPath:error:, and it is the same in iOS as in Mac OS X.  (It's funny that you already call - isExecutableFileAtPath: in the same NSFileManager class.)  Even if you weren't familiar with Foundation, you would still be better off calling the POSIX function chmod(2) rather than the chmod(1) command.

You've neglected to do any kind of error handling on the /bin/chmod task.  The operation could easily fail if, for example, the user did not have permission to modify the file.

It's misleading to name the parameter of runSystemCommand() cmd, as it really only contains the path to the file whose permissions are to be toggled.