The list that linked above is not one to follow. This guy suggests freezing "authentication" apps. That will cause the problems like you are mentioning.
This thread at Post #10 mentions what appears to be much safer list.
However, I am going to ask if the guy who created this list still feels that this is a safe list. I still wonder if deleting or freezing backup assistant will cause undesired problems.
Read this thread, Uninstalled Contacts Storage and now im screwed
it explains how to replace system files if you are able to operate your phone. Pay attention to the instructions in Post #6 and then read my notes in regard to the procedure at Post #17.
I don't think a factory reset will fix the issues that Titanium Backup is creating. One other thing I found out today, Titanium Backup does not seem to actually backup apps, it only saves the data from them and creates a download link from the market. So if you delete a system app or "Bloatware" but think that you backed it up first with TiBu, you will be unhappy with the result when you try to restore it since its not in the market for download.
Hope this helps those are freezing or uninstalling apps with TiBu.