for an alternate command line separate from the regular log in so you can do maintenance.
That would be invoking Terminal while Mac OS X is running.
But as you describe the problem, 'an alternate window while the main system is running' does not meet your criterion of having Finder NOT running.
Using Recovery does meet that test, because it is its own primitive Boot partition and uses nothing from the main system partition.
--------
This might be another way to proceed:
Another interesting feature of Mac OS X and older Mac OS systems is that once files are opened, they are referred to by File Numbers, not by Directory locations. You used this in Mac OS to "set aside" System Extensions (or .plist files) by hiding them inside another folder or moving them to the desktop, where they continued to work perfectly UNTIL the System/Application was restarted. At that point it did a new Directory lookup, and the replacement file (or no file) was used instead.