There are lots of religions that see one god with different aspects or representations, some male and some female
for example, wicca worships a goddess that represents nature, which is also a god, that represents the animals
at the same time, that goddess has 3 representations, Maiden, Mother and Crone
The kilrathi might see Sivar as having different "faces", one of them male and another female
Also, it could simply be that different cultures/religions see Sivar as a different sexs. Sivar could very much mean "god" translated literally, and simply be the kilrathi word used to mean main god or something like that
Another posibility is that when it was refered to as goddess, it was refering to an entirelly diferent god (I really dont remember where it is mentioned as female, but since I just re-read end run, fleet actions and false colors, Im guessing its in action stations)
An important note here is that females are the keepers of the Kilrathi religion (as seen by their priestesses). Sivar may be seen as a female in this case simply because of the culture related to females as keepers of the faith, to be talked about as a goddess
But to tell you the truth, the first positibily is the one that seems more probable
K