This seems extraordinarily unlikely unless you made a mistake.
OBVIOUS SPOILERS BELOW
When the PCs enter the straight corridor leading into the hall where the villain is located, they are 80 feet away. The villain has 120-ft. darkvision. The villain likely doesn't have line-of-sight for the full 80 feet due to stairs, but he can still see them in the corridor before they even get to the hall. There is no where for them to hide in the corridor, so they can't approach by stealth. If they are using a light source, so much the worse.
Once they enter the hall, the PCs are still 40 feet away from the villain. The "low-level boss" the PCs need to deal with to complete their mission is between them and the "villain." He has better sight lines down the corridor and 60-ft. darkvision. The villain has a "pet" that also runs interference for him. The pet has 60-ft. blindsight and Speed 40.
The villain has AC 15, 71 hp, and plane shift. He has the ability to, uh, turn any PC who gets in his way into an ally, and the DM is specifically instructed that this is what he will do. The DM is told that the villain leaves "upon seeing the adventurers."
To reiterate, the encounter specifically states the villain wants to escape. Given the situation, there is approximately nothing a 1st-level party can do to stop him. Therefore, the villain TPKs the party only if the DM changes the rules of engagement.
ETA: In fairness, if the PCs "took the back way in," I can see how the situation could be more fraught. Given the villains capabilities, however, even this couldn't prevent him from leaving whenever he wants.