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].