The normal alarm level for a guard is 100 already. Not sure why you'd want to set it higher than that?
Anyway... Yes, changes to the object (like SetAlarm) will persist. If you want it changed back after a certain time, you'd have to change it by script. That's kinda uncertain though, b/c any NPC of that ID that the player encounters after the first set but before the reset will keep the higher setting (I think).
OK that wasn't all that clear... Try again
If the alarm setting of a specific reference is stored (which happens when the player encounters it in the game), that will take precedence over general object changes, so to change that you need to set the alarm of that specific reference (e.g. in dialogue or targeted script) - and that setting will only carry over to refs the player hasn't encountered yet b/c it also changes the object. At least, I'm assuming this is the case (haven't tested alarm, but that's how it works with e.g. SetHealth).