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I'm applying to a USAO job in a less competitive office. That particular office wants several references, but I don't want the partners at my firm to know I'm looking for alternative employment. I interned at a government agency after my 1L year, but my former supervisor at that job probably barely remembers me (this was a few years ago, and they hire a handful of interns every year).

My current plan is to list two two junior associates who worked with me on the same matters.
They are the same class year as me, but I don't trust many people at my law firm to keep their mouths shut. I could email the former supervisor who probably doesn't remember me and ask him as well- it may be my only option at this point to find a third reference. I'm not sure what else to do....would this completely screw up my chances, or does this sound reasonable? Do I need to bite the bullet and loop in a partner at my law firm to be one of my references? I don't trust any of the partners at the firm, unfortunately. It's not the greatest environment.

I’ve been in this situation and just used associate references for the initial application, with a note at the bottom that additional references were available upon request. If/when you get to the actual interview stage, then you can explain the situation and provide partner references. I think this is a common situation, and most folks are pretty understanding about it.

AUSA here. For what it's worth, our office doesn't contact references until toward the end of the process after the final-round interview with the U.S. Attorney. I would start to think through whether there are any partners that you trust even half-way, or at least would give a positive reference rather than tanking your chances. By the time references are contacted, it's mostly just a final check to make sure no one says the candidate is a psychopath or a terrible lawyer or colleague, the office wants to give the offer.