I wouldn't delete it, that's almost certainly going to cause more problems than it solves. If you want to see what happens then you could try renaming it to something like 'safaritool.deactivated' but be very careful messing around inside packages, especially system ones.
Something you could try if you haven't already is this tip by Marcia G. in this
thread:
Open your .Mac preferences in the System Preferences.
Choose advanced pane.
Press Reset Sync data...
Set Replace to your bookmarks
Choose the direction .Mac to your computer and press replace
Just ignore the last two steps and make sure it isn't set to do anything with bookmarks after the reset.
Have you ever set it to sync your bookmarks? It seems like something's stuck...
If you can find the right keychain entry then I suppose you could change it's access to "Allow all applications to access this item" which would probably stop it asking you every time, but this seems a bit of a security issue if you can't find out
why it's asking...
Apologies for not being able to offer anything else (I don't have a .mac account to test with unfortunately).