That stored proc generates server stats, and depending on the stat results, it will fire off the alerts in SQL Server. If that instance of that stored proc hangs or has abnormally high CPU, just kill it. The agent will fire it again when needed.
Also, by default, SQL Server comes with a set of alerts that the server can use (called, “Demo”). I would keep the alerts active if possible and see what alerts are being triggered and why – check logs.
There was also a bug on SQL Server 2008 that was fixed that stemmed from this proc causing high CPU, even if all Alerts are disabled. I’m not sure if this fix applied to SQL Server 2000 with latest SP.
More details: http://connect.microsoft.com/SQLServer/feedback/details/536354/execute-msdb-dbo-sp-sqlagent-get-perf-counters-hogs-cpu-although-no-alerts-enabled#details