Yes, switching Aliases would - temporarily - switch or remove the Factions that "Actor" is present in.
So, you would have created an NPC in the CK, named MyActor (or named whatever you want!)
Then you would need a REPEATABLE quest in which you create an Alias (and add that Alias to whatever Factions you like ... On the Quest Alias Form) ... and then assign MyActor (the ActorBase) to that Alias.
Then you would need a second REPEATABLE quest in which you create another Alias (and add that Alias to whatever Factions you like ... On the Quest Alias Form) ... and then assign MyActor (the ActorBase) to that Alias.
Now, when you want to make the switch, you STOP one Quest and START the other. And the Actor will take on whichever "role" is specified in the ACTIVE Quest. As soon as that Quest stops he will go back to being his normal self.
So, you can also have what you might call his "normal" behaviour on the actual Actorbase object, if NONE of your switch-quests are currently active the Actor's behaviour will be whatever packages you have on the actual ActorBase (the NPC in the CK).
You could also have many, many switch-quests ... And those quests can have roles for multiple NPCs. So you could have, for example, a group of Imperial Guards who, at a trigger you script, switch sides and go on the rampage, wiping out their fellow soldiers ... and then flip back to "normal" when you flip another switch (
this storyline is Apple Copyright ... you will be sued for billions if the ghost of Steve Jobs evens smells that you might be getting close to using it! 
).
If you want to alter the Actor's base stats - those you find on the actual actor-form in the CK, like HEALTH - then you attach a script to the alias, that fires at a particular stage of the relevant switch-quest, that alters those variables. In the final stage of that quest - your shut down stage - you revert those values back to their normal state (again, in a script attached to the alias).
Watch out for QUEST PRIORITIES. A single Actor can't be two people at once (well, they can, but obviously you will get conflicts), so the routines - the ALIAS - that take presidence are the ones in the Quest with the HIGHER Priority. This can cause you troubles ... the Actor will still attempt to be two roles at once, and so can exhibit some odd behaviour. It's good practice to only have one switch-quest active at any one time ...
The way I look at it, Actors (NPC) - called BaseActors, most of the time ... apart from those based on Templates - take on Roles (Aliases) that you write for a Story (Quest).