It has nothing to do with saying anything about Zoro. When I read the manga and watched the series, I instantly understood it as this. It took no thought or analysis to it. The fact others weren't seeing it as that, confused me. It makes no sense to be speaking about not killing him since Zoro already knows he didn't kill him, the crew already knows he didn't kill him, Kuma already knows he didn't already kill him. That's not how conversations work.
In sentences you have a subject/direct object and indirect object. A person in a convo answers the direct subject of the conversation, not eluding to something similar. Kuma is speaking about surviving the bubble when he states 'still alive.' Surviving is the subject. So Zoro answers about the bubble, the subject of the conversation. Going off topic to say mercy for the whole deal is just being redundant and switching to an indirect object.