Ninite Pro can uninstall applications too. Just use the /uninstall switch.
Here's an example command to remove iTunes from the computer you run it on:
NinitePro.exe /select iTunes /uninstall
The /uninstall switch also works with Ninite Pro's remote mode:
NinitePro.exe /select uTorrent /remote file:machines.txt /silent report.csv /uninstall
This would remove uTorrent from any machines listed in machines.txt and write a CSV report of the operation.
These features are only available in Ninite Pro Classic.
We're working on documentation for the new Pro web interface. For now the available help for that is inline in the interface.