Nope, by doing that autorun.inf could not able to write himself into pendrive due to the folder with the same name created by Flash Disinfector (sUBs) And by create a empty folder will not take even 1kb space in the pendrive.

Your way to do is prevent the malware infects your data, but sUBs's way is prevent the malware goes into the pendrive. So whichever better?

Since there's other malwares that possible to infect external hard drive, it's not practical to do sort of the methods just to prevent the intrusion of just a kind of malware. autorun.exe can be prevented by right click and choose Open or Explore on your pendrive instead of double click it. Very simple.

Anyway your way can used to secure your data I guess. Since it prohibits any action of altering the root folder.

So the annoying part is you have to change the permission level when you want to write something into it...User unfriendly...