rvbinder, go back a few steps and make sure all is well with your installation of multisite. Revert to a working state. And as an aside, you do test your code edits on a sandbox, not a live site, right?
If you are not comfortable editing existing plugin code, are you comfortable creating your own plugins? If not then I agree with you "commenting out code to alter behavior is not good programming practice". Leave the plugin alone, then.
Saying you see the "the same confusing behaviour" as the op, then applying old suggestions/changes to current code to a live site without a means to back up is what got you into trouble here, I figure.
The plugin works as intended out of the box on a clean, unedited, Multisite installation.
Try it on a vanilla install, a sandbox, of your own before going live with it. You are a network admin, so tinker away in your sandbox, fork it to your heart's content. Do not roll out anything to your live site till you have it well under control on your sandbox setup.
You said you "Tired deleting the plugin files, cannot login". How closely did you read the installation instructions for this plugin?
Have you created an "mu-plugins" directory? That is where you should be looking to delete it then.