How to undo misoperation of Reinitialized existing Git repository

No need - it is quite safe to do. From the documentation:

Running git init in an existing repository is safe. 
It will not overwrite things that are already there. 
The primary reason for rerunning git init is to pick up newly added templates.

The templates are files such as the sample hooks and example files that are part of git. If you have updated git since creating the repo and these files have changed, they will not be updated - only new files will be added. Since none of these files are actually 'active', this should be entirely safe.