I feel for the both of you, as you obviously want to overcome this obstacle but it seems so daunting to overcome.
Everyone else replying has given you great information. There are different options available for treatment. Medication, diet, homeopathic, etc. These can and are often combined. Discussing with your GI options available to you is essential.
There is currently no cure for Crohn's, including a re-section. No matter what a person does for Crohn's, it can come back. It is very much treatable but curable. Many people live by a certain treatment and have been put into remission for the rest of their lives. It's absolutely possible. The same treatment, on the other hand, could have done nothing for another person. Crohn's is a complete crapshoot.
You have a lot of questions. Good for you. A lot of new-comers don't think of asking the basics, for a variety of reasons. Knowledge is power. In this case, that statement cannot be more true. The more you know about the disease, the medications, alternate therapies and diets the better off you are. It is a HUGE difference.
Asking questions on here or other similar sources is excellent, as we can give you personal anecdotes and first-hand experiences that most doctors can't. At the same time, you MUST ask your GI questions. Anything logistical, technical or the like needs to go through him. If, for whatever reason you cannot communicate properly with him (availability, personality, lack of knowledge), seriously consider finding a new GI.
I am certainly not the best un-professional authority on Crohn's and pregnancy, but I will have to agree that having a good handle on your Crohn's prior to becoming pregnant is very important. I cannot imagine being both pregnant and dealing with out of control Crohn's at the same time. All the same, as others have said, pregnancy has been known to induce remission. However, I really believe that having good, solid control (both physically and mentally) over the disease is really the first step that needs to be taken. By complicating a non-ideal situation with another intense possibly life-altering situation, you can only imagine something will somehow suffer.
That brings me to my next point. I am going to be completely blunt here. You seem to be in a good frame of mind with the diagnosis. How is your wife handling it? Everybody handles a medical issue in a different way an everyone grieves. It seems as if your wife might not be mentally dealing with it too well. Again, this is coming from a complete unbiased observer based on what you have said in your posts.
You've said yourself she's very depressed; yes, the depression could be due to medication, but my guess is it's real depression. She doesn't want to take the vitamin D because she says it makes her nauseous; however, vitamin D does not cause indigestion problems. Could she be having a problem getting around the fact that she needs to take medication? So that she does not have to take the medication, she instead blames a problem on them. I really am trying to be delicate here- it just honestly seems like she's having problems accepting/in denial with some depressed moods.
It is not bad to be depressed with a chronic disease such a Crohn's. More often, it is actually the norm. From what I have seen, approximately 75% of those with Crohn's/UC have depression. I really want you to consider this and talk with your wife, as depression can be helped. Discussing any emotional or mental problems with a professional would allow you to understand your options. Treating depression doesn't mean going on medication. Otten times, realizing you are depressed and talking about it is enough to get a person on the right path.
Not wanting to do the things one loves doing is typical of depression. Exhaustion, change in routine and general tiredness/fatigue are also typical symptoms of depression. Just like you said, the lack of interest in everything could definitely be medication. But it also could be depression. Please consider the possibility.
Have a frank conversation with a doctor you trust (hopefully your GI) about everything your wife is experiencing. Discuss her moods and feelings and definitely talk about properly managing her Crohn's both in the long term and short term.
Depression isn't a reflection of a person. It is an illness. Just like Crohn's is an illness.
I really hope I explained a much as possible. It seems your wife might need some extra love and support during this time. I hope I did not come off as a mean bully. I hope I gave you an outsider's perspective and that it may help both you and your wife. We are here in any way we can provide support and keep asking questions. Good luck on this journey.