They'd never die because Pokemon genocide for shock value of all things is a terrible idea, but a focused attack by Team Rocket on Ash's Pokemon would be a pretty interesting mini-arc. His Pokemon are of decent quality, he has a fair amount of them, and Jessie and James can attest to the fact that he's beaten them numerous times so there's definitely some merit there. The biggest problem would be that Ash would have to be in Kanto at the time so he could actually partake in the rescue. Having Team Rocket steal his Pokemon and then bring them anywhere near him would be a bad move on their part.
Chances are he'd just be left with what he has on hand and that wouldn't be a problem except the entirety of Team Rocket would be against him. Maybe there'd be a giant team-up with him and the trainers who most impacted his life throughout his journey. Maybe it'd all make a better movie than a mini-arc. It's a good idea, though.