Thank you for writing such an engaging story.
It is an interesting moral debate. Especially since she can not have it with anyone else. Bouncing ideas of other people, especially if they have other opinions helps avert tunnel vision. And despite her forge granted Genius I doubt Sophia is exempt from it. Morally speaking, I think that it would have been a good idea to get a second opinion. Also from the point of view that she might miss other important applications. Ceph Nanotech together with her abilitiy to program it could have been a straight up victory condition, even if she never uses it as a Bioweapon. Just using it for selfimprovement, faster healing, unaging, etc. would have been a major step. Not even talking about using the Grey goo to outproduce their enemies, a potential she took from the table for now.
On the political and interpersonal point of view: "Hey Professor, what would you consider about the ethical implication of a potential grey goo swarm that can be programmed as a Bioweapon against the Vilani. With a delayed kill switch to ensure we got them all." is not what you want to hear from a student that got herself noted as a Genius with a Major microbiological discovery and expertise as well as incredible programming ability to her name. Especially after she got unsupervised Lab time with top of the Line equipment. Even if you are in favor of it, the implication of what she got up to are kind of concerning.
Practically speaking she has the Celestial Forge. Discarding one option, even doing it in a final way like this shoudn't matter. Even just taking a short look through the forge in use here means that there are many incredible exiting things that could give her what she needs from the forge. I don't know the setting so I don't know how long she has before the war starts. Though I think it would be possible for Sophia to develop the Jump-3 Engine by the time she is finished with University. It would certainly be something very interesting to write her Doctorate over.
Regarding Sophia's studies, what is she nominally studying right now? It looks to be something like Microbiology given that she got unsupervised access to a University lab for it. We know that she has a wide pool of advanced scientific knowledge, but others might slot her into that niche. Also is there going to be any interaction with her peers beyond the second hand note we got?
Her decision what to do after, found her own company or take a job with the military or a company will be something I also look forward to.