I confirmed this works with Zetacoin as well.
The Wallet and Client need to be closed before any edits can be made.

Installed on Windows 8.1 64bit (in this exact order to their default directories):
python-2.7.6.amd64.msi
Twisted-13.2.0.win-amd64-py2.7.exe
zope.interface-4.1.1.win-amd64-py2.7.exe
ez_setup.py
pywallet-master.zip

The files in the pywallet-master.zip were extracted to C:\Python27 and then I created a .bat file that ran "pywallet.py --web" (no quotes of course)
Then used Chrome to open the http://localhost:8989 or just localhost:8989
Then clicked the top bar / menu option of "DELETE"
And filled out the form as directed but with the Zetacoin wallet.dat file info.
Clicked the Delete button on the bottom of the form.
After it deleted the transactions, I selected the QUIT option on the top bar / menu. This closes out the DOS window in the background and the webpage goes to "page not available".
Created a shortcut to the Zetacoin-QT.exe file with the added line of -rescan. Opened the shortcut file. Zetacoin splash screen loaded and after a few minutes, only the confirmed transactions were there and the one transaction that was "unconfirmed" for a few days was gone.