Don't understand your post.
Fill in the blanks for me because it's been a while and cba to watch 2 hours of footage.
Step 1. Fireflies attack checkpoint.
Step 2. Fireflies decide to leave and escort Ellie.
Step 3. They recruit Joel and Tess and have them escort Ellie to the agreed meeting point.
Step 4. Fedra arrive at the agreed meeting point after Joel and Tess find the Fireflies dead (by zombies right?).
Is there anything I'm missing, you mentioned that some Fireflies were captured, did we see that and was that before Step 2? I vaguely remember that happened near the start.
It doesn't really matter if they are a Terrorist group, if they leave your city then brilliant. They can go and die on the outside instead. There's very little point in risking valuable equipment (humvee as per the video you posted) and men in the hope that you can catch up to them and kill them. Knowing that to do so would mean you would also take casualties yourself and worst case scenario risk losing all the men and vehicles. It's an unnecessary risk with little reward as the cell was leaving the area anyway.
1. Fireflies attack checkpoint.
2. Fireflies are tracked and ambushed by Fedra. Marlene escapes.
3. Fedra interrogates captured fireflies, finds out about extraction point. Send force to stamp them out in the area once and for all.
4. Fedra arrive, they kill the fireflies that were there, then patrol the area for any stragglers.
5. Joel, Tess and Ellie turn up.
I didn't say they were, I said they could have been. Again, we don't need to be spoon fed every single detail to understand how a thing happened. The motivation is there and thats enough to explain why it happened.
They aren't dying on the outside though. They keep coming back. So it makes sense to finish them off.
Risk of equipment and man power, to you and me maybe. But if your men had just been killed, if you were sick of the constant threat, maybe you and I might see it differently? Might also just have been that the guy in charge was a dick.