I am interested in employment with the CIA, specifically in clandestine operations overseas. I have just begun doing research on this, and still know very little, so forgive my ignorance. 
I will state my background. Please tell me if it is worth for me going forward, and the general likelihood that I may be considered/accepted. Thanks!

I grew up in the private school system (Christian school). After high school, I joined the Marine Reserves in a combat unit. I was sent to Iraq in the initial invasion. Recieved the Combat Action Ribbon and Presidential Unit Citation, to list a few. Since joining the USMC, I have made several trips to a US friendly country in Asia, visiting my girlfriend who is now my wife. I have never done any drugs, I have had alcohal a few times, been really drunk only once. For me, my faith is incredibly important and I try to live according to it. 
I am a university student now, English major with a 3.49 GPA. (I don't intend on applying until after I graduate). 

Key concerns are these: 1) My wife is a foriegn national. She is now a legal resident of the USA, but is not a U.S. citizen. Obviously, that means my in-laws are not Americans. 
2) I have not been married long, and was struggling with the pressures of marriage, etc. etc. and had gone on a trip to her country (she stayed in the US while I went there), and there, I had sexual relations with another woman. Since coming back, I told her everything and we have worked it out, and moved on, however, I am concerned that this will be a tremendous character stain from the Agency's eyes, and make them unwilling to hire me. 

Sorry for the long-winded question. I really don't know much about the process, or if I am even Agency material, or if my fatal flaw is too much for them to endure. 

Any and all responses are very much appreciated. Thank you.

I am just wondering if I am Agency material or not, and if my fatal flaw will keep me from consideration. As I said, I am still researching. I am very much interested in fighting the war on terror, but not in the current military capacity which I am in. Gathering information covertly for this cause does not conflict with my spiritual beliefs. (I really don't want to get into a big political/spiritual debate here). 
So for sure, my wife must become a U.S. citizen? We both have no ambition for that, since there are numerous benefits to here staying a citizen of her home country. 
Also, I am not unsure of the Agency's standards on who they want working for them. My IQ is somewhere around 110, nothing special, my academic performance is decent, but now outstanding. As for work experience, I am very limited, with the exception of the military.

If your wife wishes to keep her native citizenship, then don't even think of applying for CIA employment.

I appreciate that you may not want to get into a political/spiritual debate on this message board, which is why I didn't ask you to answer such questions here, but were you to go to work for the CIA, you would at some point have to come to grips with the fact that the CIA is involved in crimes such as kidnapping, torture, and murder.

Regarding whether your sex life is any of the U.S. Government's business, the ball is only in their court if you decide to make it so.

George is right:  your wife must at least be on a path to citizenship (i.e., forms files etc) for you to be considered a candidate.   

Second:  if your wife is from an unfriendly country (China, Russia are the biggies), then even if she is a US citiizen this will pose problems.  May not be the death of your application but will definitely make the processs longer.

The stuff regarding your sex life would not be responsive to any questions on the security forms you need to fill out.  The shrink may ask something to that effect.  For them the key for situations like that is that there is no possibility for coercion--in other words, that somebody couldn't hold out the possibility of telling your wife about it if you didn't do x or y...think of the movie the firm.  In your case, you wife knows about it so that would be moot.  It would go to character but this can be mitigated by time passage.

Good luck.  Just go ahead and apply and give it a shot if you are really interested.