Did Daisuke Serizawa do the right thing?

Serizawa was backed into a corner. He didn't want to detonate the Oxygen Destroyer at all. It was Emiko and Ogata that convinced him--And in doing so it gave him the only out to make sure humanity wouldn't use it.

Leaving Tokyo Bay barren vs. giving the Cold War more to flex over seems like a no-brainer decision.

For some reason I second-guess everything. It might be because morally grey choices really scare me. I really dread the day I’ll have to make one.

I honestly agree that it was the best choice he could have made in that scenario. It must have took a lot of courage to make that decision, and to do what he did to kill Godzilla. 

Daisuke Serizawa was, in a way, forced to use the Oxygen destroyer. He didn't want to, but he had to use it

Yes he did the right thing,Emiko and Ogata convinced him though.

It was a good choice after being convinced. Godzilla was a great threat, he even sacrificed him self and his lab stuff to make sure ppl don't use ideas to harm others. Even though destroyah was created anyway years later but I guess during their present it was important to finish gojira it was a bad idea for the future because of destroyah but gojira was the only threat at the time so yes even though he didn't want to necessarily do it he got convinced and did it. 

Yes, but Destoroyah only happened in one continuity. Not any of the Showa, Millennium or Reiwa films.

After Ogata found out, if Serizawa hadn't done it himself someone else likely would have. Then the compound would have definitely fallen in the wrong hands.