Sounds like a good idea in theory. In fact you could certainly destroy anything and everything possible and attempt to remove the influence of entities from your levels if your gameplay moves the player only forward in a level in a linear fashion. Not such a good idea if the player is able to move backwards in a level by choice and find that many entities are missing. You can always respawn entities if you need them again.
Allowing a player to move backwards in a level can be useful as it can provide opportunities for the game designer to add further tasks for a player to do in a level and make the level seeemingly bigger or at least take longer to complete. This can be important in an engine which has such a very small world size as does FPSC particularly to those who want to develop a game of seemingly large proportions.
The answer therefore is if you wont need the trigger zones after use then theres no particular reason for keeping them so try removing them and see if it helps with fps. It can do little harm. Same goes for any other entities that you may be sure you will not need.
The main difficulty is with Characters you can spawn them and remove (destroy) them - as many as you want in a level but that will not overcome the main restriction of numbers of Characters in view at any one time. If you spawn too many (which you may think a reasonable number) at any one time your fps rate will fall very quickly and gameplay will be badly affected in many ways.
This situation may change in future but that is very much uncertain at the moment.
"There are those who said this day would never come - What have they to say Now?"