That checkbox writes/deletes the registry entry
HKCU\Software\Microsoft\Windows\CurrentVersion\Run\TortoiseSVN Monitor
if that entry is still there even if you uncheck the box in the dialog, then you can delete it manually with the regedit tool.
however if you configured it to auto-start some other way yourself before, you have to remove that yourself.
You can use the autoruns tool from sysinternals to figure out how/where the autostart happens.
Stefan