Using leaked proprietary information in scientific paper

Sounds like you have found an interesting source and are considering the moral implications of using it. What I will say is based purely on personal opinion and probably what I would do unless instructed otherwise.

Leaks are a fact of life. With the proliferation of digital material they are commonplace. Look at Wikileaks, the Snowden revelations etc. Once material has become public there is - fortunately or unfortunately - no going back, regardless of how that information became public. It is the responsibility of the owner/creator of the material to ensure it says secure.

Dissemination of such material could be highly fruitful - but think of it this way - will your publishing research based on the material be ultimately constructive or destructive? Will it benefit just you or the wider world? Who is it really advantageous for? If the answer is just you, I would probably withhold your research based on it. If it has wider ramifications of great import, go with it. Also consider the reasons why it is confidential. Who does it serve - who does it protect? Was the confidentially because of financial reasons, incomplete research, company policy, or 'national security'?

There is a heavy moral tinge to this question, and you may have to do some soul-searching. But ultimately, if it serves the wider discipline in a positive way, and such servitude grossly outweighs the few individuals who it would ire, I would use it, as long as there are no legal implications for yourself [unlikely since a third party leaked it, but you can never be too careful].

I'm glad I'm not in your situation. It's tricky. While I can't really offer the ethics of scientific publication for this situation, a journalist, which is a constitutionally protected entity in the US, would probably publish after soliciting comment from the company.

You, however, would probably be sued, as would your university. If I were in your situation, I would probably consult university counsel, and abide by whatever they tell me to do. If the school won't cover my back, I wouldn't want to assume the personal liability.

I suppose another way to look at it is by how important the matter is. Is it worth the s***storm you're likely to find yourself in?

Have you asked the editor of the journal? They might be unwilling to publish your paper because of the risk of being sued by the company that had its proprietary material leaked. They might also argue that the source shouldn't be cited because it might disappear at any time and wasn't really "published."