Are we doing something wrong? Isn't this a little too powerful?
Possibly the humans did something wrong by letting the base get so much damage that you could destroy it with 2 failed tasks, but a little bit of bad luck (failed repair rolls) can get you into that situation. Maybe they were a bit too slow to spot you were infected. Perhaps they made poor choices on which task to do - I've noticed some people tend to choose whichever task is easier to pass without paying enough attention to what would happen if the task failed.
If you hadn't managed to end the game on your turn it's likely the humans could have turned things around. They can now issue orders freely, which basically gives them 6 actions to your 1. They should be able to quarantine you and repair a reasonable amount of damage before you get another turn .
Also, if the Suspicious Activity cube moves all the way to the end of the track then that vote still happens, so that's another way to get you into quarantine even with the base damaged.