Using the AddIn Manager, un-checking the R# addin checkboxes does NOT result in R# not loading on the next startup. According to http://forums.microsoft.com/MSDN/ShowPost.aspx?PostID=167838&SiteID=1 this is because the addin is registered under HKLM rather than HKCU.
I had to change the HKEY_LOCAL_MACHINE\SOFTWARE\Microsoft\VisualStudio\8.0\AddIns\ReSharperAddIn2005\LoadBehavior registry value manually (to 0? from 3). Assuming Microsoft doesn't fix this limitation, this tip might be useful in the final documentation.
(Build 215 for vs2005, by the way)