You can idle it if you leave the little green ones. Obviously you have to be able to make more than they take, but the max etrions (bacteria) on the screen is 33, and the little green ones take 100 each, so the max they can take if you fill the screen with little green ones is 3.3k. Then the big green ones max is 33k, then 330k for yellow, etc. The important thing is to not use the Auto-killer until you know you can handle the bigger ones.
My issue is when the bigger ones come in faster than I can kill them at higher transcendence levels, which is manageable but tedious. As soon as you get one on the screen that you know you can't kill right away, exit the save and reload. The game automatically saves every time you exit (through the menu, not closing the game) so when you load back in, you have a clean screen and your sylphs and other progresses are saved. Like I said it's tedious, but if you focus on fluxells, Luminettes, and Celestines, eventually you'll be able to just let them go, killing off the bigger etrions and leaving the little ones.
Idk if this counts as cheating or exploiting, but if the dev didn't want me to do that they should've made a better balanced game. Otherwise it's literally impossible. Besides, it's an offline game with no rankings, so fuck you anyway, I'm cheating.