That unfortuantely doens't solve the problem of an sv_restart or the like being used and overwriting people's score.
Could you maybe write in a thing that if the commands sv_restart, sv_restartround, quit, restart, or kill etc are used it backs up the scores and sets everyone's again so they don't lose theirs?
Unfortunately a server shutdown or restart doesn't use any HL command so I have no idea if that would fuck up scores too :\ I'd just have to be careful to do it when no one is in the server.