Thank you for the information and your question. You can read the AFI on fraternization, and other "unprofessional" personal relationships, at the following link: http://static.e-publishing.af.mil/production/1/af_ja/publication/afi36-2909/afi36-2909.pdf
But, to summarize, dating and sexual relations between officer and enlisted, regardless of whether they are in the same chain of command or location, is per se a violation of fraternization rules. The fact that they get married is not a defense, nor is it proof, in and of itself of fraternization. (Please pay particular attention to 5.1.3 and 126.96.36.199 of the instruction). However, at NJP, for example, the proof required for punishment is only a preponderance of the evidence, which is more likely than not. Therefore, it wouldn't take much evidence to establish a dating relationship and the CO does not have to suspend their common sense in order to make the decision.
All that said, it is not uncommon, in the AF, for CO's to look the other way with officer/enlisted marriages as long as it is not an issue otherwise (same chain of command or causes rumors or trouble of some sort independent of the issue itself). But, that is not a guarantee that your case would be one of those that would be ignored. That I can't say and it would be up to the respective CO's of the two servicemembers. The way the instruction is written though, the onus is more squarely on the back of the Officer though in the relationship. So, that means it would be more likely that any consequence would be against the Officer in the relationship since they are held to a higher standard. But again, you can read the instruction yourself and see that unless there is absolutely no evidence that the two servicemembers involved have ever met face to face, which is doubtful, there is always a chance that their marriage could result in an investigation and potential punishment for one or both.
Whether the chance is worth taking is up to the servicemembers based on what they know about their respective CO's and their attitudes about these issues. Please feel free to ask for clarification if needed. If none is needed, then if you could take a moment to leave a positive rating in the box above, I will receive credit for assisting you today. Thank you