I don’t want to get alerted due to occasional CPU spikes that may hit thresholds. Can SapphireIMS take care of this?

Yes, SapphireIMS provides option to the user so that he/she can configure the tolerance limits in the thresholds before generating the alarms within the time period. Please refer our online help link - Thresholds

Also, we have option to configure dynamic threshold. Please refer related article - How Static and Dynamic threshold works in SapphireIMS?