My personal opinion is that the thread you reported is one that should not be deleted. As such, it was appropriate for it to be marked as "bad".

In my experience, there is a bias of moderators to mark reports as either "good" or leave them as "unhandled" when they are "bad" as a means to help users' reporting stats, and to avoid conflict with those who are active in reporting posts. I disagree with this mantra. I want to be informed when a post I report should not have been reported so I can use that feedback in my subsequent reports. If I disagree with how a policy is being implemented, I can open a thread in meta arguing to change policy.