Yes, it's certainly possible to use "nascent" in a negative context. But given its clear (etymological) relationship to babies and birth (typically happy events), to my ear, it lacks a certain gravity, foreboding, or ominousness which you may (or may not!) be seeking. Let me suggest a couple alternatives.
I've always liked the word "inchoate" for its sense of imminence and inevitability overlaid with a strong feeling of "unformed-ness" (not-ready-ness?).
inchoate: just begun and so not fully formed or developed; rudimentary.
There is also "incunabular", which is (in my experience) usually applied to early books and writing, but one of its dictionary definitions is:
incunabular: earliest stages of something; beginnings
The words inchoate and incunabular both seem foreboding to me. The former evokes in me the idea of some Lovecraftian monster struggling to be born (just pecking at its cosmic egg; I actually often confuse this word with "chthonic"), and latter is reminiscent of incubation.
So if you're trying to write apocalyptic plague fiction or a clinical description of a patient with early signs of a disease that's sure to develop (using his body as an incubator), one or the other word might suit you.