It seems you are bothered by what happened to Rebbi Eliezer, Raban Gamliel, and the world.

Of course, Rebbi Eliezer's words are Divrei Elokim Chayim. However, Raban Gamliel felt he could not leave Rebbi Eliezer to continue to teach his opinion because of concern for weakening the Sanhedrin's power and respect, as others might follow his powerful opinion! So even though it meant paining Rebbi Eliezer, and even though paining him was dangerous because Hash-m would avenge his pain, it had to be done. So the destruction of produce was quite inevitable, and Raban Gamliel's death also happened. (Rav Chayim Shmuelevitz explains that hurting someone is like entering fire: you get burned as a result; see Sichos Musar 5731:24.)

All the best,

Reuven Weiner