Depending on which Safe Mode you're going into, it's easy to recover from this with a simple registry hack:
Safe Mode with Networking:
Create a new key here called MSIServer and change the "Default" value for it to "Service". Then run "services.msc" and start the Windows Installer Service. You'll be able to run SafeBoot in any of the Safe Modes.
I personally prefer this as sometimes I'll need to run application installs in Safe Mode that require Windows Installer. Not exactly sure why SafeBoot isn't a standalone executable but this is another workaround for those stuck in Safe mode boots after using this tool.