Vamshi,
I just tried uninstalling Bookmarks on a clean 4.6 installation with .LRN and had no problems. What I usually do in these situations is uninstall the package in the APM with the sql drop script un-checked. The APM will then unregister the package from the system and I've never seen this fail. To remove the data structures of the package you must then step through the sql drop script and execute the statements manually in psql.
Your problems stem from a mismatch between the create script you ran when you installed the package (when was this?) and the drop script you have now. You might have updated the sources after installation and forgotten to upgrade the package in the APM. Another possibility is that the package was missing an upgrade script.
