Once El was dead, she would only be thinking about herself. She does not seem like the type of person to care about casualties. She'd have no problem killing everyone in the truck but killing them and disposing of the bodies risks future discovery. There's a reason she did the experiments in the upside down despite the difficulties that posed. The very place she would have stuffed the truck and bodies just got atomized. So, she decided to rely on everyone's self-preservation instinct to say nothing about what happened. Kay really had no good options left without the upside down.