That file stores settings for each site so that the service knows how to import things. If it's not writable, you won't be able to add new sites and actually have them import.
A few things to check, in order:
First, the SmarterStats service does need full control over the install folder (specifically the service folder and all subdirectories). It could be that those permissions were reset when the installer did its update. This is especially true if you changed the service to run under a different user account.
Second, I know it's cliche, but a reboot may help. It's possible the sitelist file got locked and just needs a restart to unlock it. If you want to investigate this first before rebooting, try running a utility like http://www.dr-hoiby.com/WhoLockMe/
Third, if you have an anti-virus, exclude that file. To prevent loss of data in case of power failure, SmarterStats writes this file by writing first to a temp file, then renaming the old file to a backup, then renaming the temp file to the actual file, in rapid succession. Your anti-virus may be triggering on the file during these operations and locking it for a scan.
Lastly, check to make sure that the read-only flag didn't somehow get set on that file.