While a civil Marriage is not encouraged and has some consequences, it is better than living in "unmarried sin". Before everyone jumps down my throat ....consider situations where there was no Orthodox priest within reasonable distance or one that came infrequently. Orthodox people used to marry civilly and then when the priest came to their town they had a church wedding. While this seems like it should not be possible nowadays, I think that many Orthodox people still find themselves in similar situations.
Also sometimes for legal purposes civil marriage may have to be done first, yes you should wait, but who of us is that sinless?
I think that this is a time when economia is used. Also while we are encouraged to marry an Orthodox believer, the Church recognizes that sometimes this does not happen. There are situations where non-Orthodox and Orthodox people are allowed to marry in Church. Very strick guidelines mind you.
I agree with Justin and Katya that you should speak to a priest or your bishop. That's what I did when I found myself in a similar situation.
Good luck!
Milla