Based on what I know, you have two issues:
One is your wife's residence. If they grant her residency, they want her to reside in the USA. My wife and I were married while she lived in Canada, and she stayed there for 10 months until she got her green card and for another 20 months after that. She traveled to the USA about every other weekend, but she started to get some hassle at the border about why she wasn't living here. She moved to the USA shortly before she filed I-751 for removal of conditions, but I suspect that if she were still living abroad they'd have raised a greater issue about that.
The moral here being, yes you will be in a lot stronger position if she lives in the USA.
The other issue is showing a bona fide marriage after two years, when her conditional green card expires and you file for removal of conditions. The fact that you are overseas working on a contract is most definitely not an insurmountable hurdle, but I'd be attentive to the proof you will have to show. Her living with your parents is a good start. Do all you can to show a real marriage. Run your money through joint bank accounts. Have drivers licenses with the same address and get mail sent to the same address. Keep logs of phone calls if you can (hard to do if you're using Skype, but if so, do screen captures). Are you about the same age as your wife, and does she have any other connection with your family? Hopefully the answers are yes and no - if she is your parents' age and a friend of the family you will certainly get scrutiny. (Not that you've given any hint that is the case.) Hopefully you have wedding photos? Documentation of your courtship?
You didn't indicate how long you expect to be overseas or how often you intend to return. Once she gets her 10-year green card, she will have to come back to the USA at least once a year to keep it (not a hard firm rule but a really good idea).
Yes, it all seems bizarre that to get her papers to be together, you have to be apart. But what I said above is based on my own experiences with a foreign spouse who didn't emigrate immediately,