I am in the US NAVY Submarine Force, my fiancé and I want to get married, she is currently in California, she is from Peru. She came to the states with a visa (that expired) and a passport(just got renewed). Would that technically make her illegal if she stayed in the states? If we got married, would I loose my top secret clearance?
I want to marry her, without losing my clearance and being able to keep her here what is the safest way?

As long as the I-94 (small white card) she filled out at the port of entry is still valid, she is in lawful immigration status. Her visa can be expired.

If her I-94 is expired, she can still get permanent residence through marriage, under section 245(a). It forgives not maintaining valid immigration status.

See an experienced immigration attorney, get married and file immediately for her.