For a Non-EU marrying/married to a Non-EU spouse you are *technically* required to apply from outside the country and to not enter the country until your permit is approved.
It is the *employer's* responsibility to lodge your paperwork for a dependent spouse visa. They should know full-well that it's not easy to get in if you are not married. But many employers live in blissful ignorance (they've never been on the other side of the world separated from their fiance because they were told crappy advice)....
I don't think there is an easy way out unless you can land yourself a job and your own independent work permit.
The alternate method (and one which has been used before) is to apply for the fiance permit and do the 'legal' wedding in Switzerland (it's just a registry thing) and then go ahead and organise your 'real' wedding party for Australia at your convenience.
After all, it's just a piece of paper that you need, and you were planning to get married anyway... ???
I guess you are living together and having sexual relations - so what's the big deal about getting the piece of paper signed ???
Can I also suggest that your 'fiance's' employer probably never lodged any paperwork on your behalf anyway ? - they wouldn't have been able to because you are not married...so you arrived as a 'tourist' - are you registered at your local Gemeinde ? - do you have health insurance ??