You can avoid using the Sony Ebook reader software - I almost never use it - by using Calibre.
You can stop the autolaunch of the software either of two ways.
1. Run: MSCONFIG. Look for the sony reader software under "startup" and uncheck it.
2. Run: REGEDIT: Hkeylocalmachine/software/microsoft/windows/currentversion/run/
Then delete the reference to the sony software.