I'm leaving my previous answer but it is inaccurate. There are ways to do what you want to do but it is as dangerous as teasing with fire one might say.
There is a software which is capable of editing registry files from command line of linux shell.
If you have a list of files that were created by particular software installation and at the same time the list of all registry keys created and/or modified during and after installation - or even better - the registry backup from before the software installation - you could reverse the changes made in the registry by installation process.
Previous answer (Somehow I think this one is better as it will prevent more people from trying to edit Windows registry from linux - even if it is wrong ;) ):
In short - no. Not directly. You can remove some files from
partions but you cannot change registry keys directly - most of the
software out there is adding some keys to Windows registry. This
cannot be edited while Windows is turned off. However you can create a
bat(or vbs) file with commands that will remove registry keys and add
this bat file to the
startup folder of Windows users (inside their
profile) - this has a potential of removing the keys from registry if
user has proper rights and/or is able to elevate rights to level of
system admin - only then registry can be edited. Placing a file in
specific folder could be of course done from the Linux level but the
process of complete uninstall can be achieved only when Windows OS is
Take my advise and do not do it. There are better easier ways from Windows itself.