It's certainly possible your son (and daughter) could have sprue as it is a genetic disease. I doubt your pregnancy has caused your baby to have celiac, he either has it or he doesn't. I was pregnant while on a gluten diet for three of my four children. Two of those three children are confirmed celiac. We found out by doing antibody and gene tests for celiac. While all carry the gene for celiac, one son does not currently have any antibodies to gluten suggesting he is not celiac...yet. My last child was not tested because I have never fed him any gluten. He is now 18 months old and was born after three of us were diagnosed and on a gluten free diet anyway.
I chose not to feed him gluten because, as a celiac myself, I know that the damage can be horrible. Sure, the villous damage may heal but what about secondary damages? I have trouble with gastritis because my stomach sphincters are all messed up from years of undiagnosed celiac. I have to be on acid medicine my enire life or risk hemmorhagic gastritis and damage to my esophagus. My celiac children had trouble with chronic ear infections leading to scarring of their ear drums and possible hearing loss (hopefully temporarily). My four year old (who has been gluten free for two years ) still has malabsorption as well as acid reflux as determined by intestinal biopsy. Also, exposure to gluten (if you are a celiac) may trigger other autoimmune conditions. Is it worth taking the chance? Also, so many people are asymptomatic with celiac, it's tough to know whether your baby will even show symptoms. My four year old suffered as a baby before his diagnosis. He was cranky and bloated and it made life very hard. My other celiac child was asymptomatic in infantcy. In other words, you won't necessarily know if your baby is a celiac until after damages show up. He could be asymptomatic and grow poorly, or have ear infections, or reflux. Everyone reacts differently.
My plan is to keep my child gluten-free until I can gene test him (with four children, it's hard to get to the Celiac Center for testing) or better yet, find someone to perform a rectal gluten challenge. The RGC is a test that can be done on a gluten free person. A tissue sample from the rectum is infused with gluten under a microscope and if lymphocyes flood the area, voila, that person is a celiac. No need to feed anyone gluten. The trouble is, it's experimental still and hard to find someone who can/will do it. If the gene test comes back positive, it doesn't mean my child has celiac, it only means he has the ability to get it. If it's negative, there's basically no way he can ever develop the disease and then I can safely feed him a gluten diet with no worries. In the meantime, I can cross my fingers and hope a different test will come along which will help me know if my son is a celiac before he ingests gluten. If the gene test is positive and I can't find someone for the RGC, at age three I will feed him gluten and test him after six months. If he comes up negative, like my oldest son, I will retest every two years to make sure it hasn't triggered in the meantime.
For my son, I have to think he's not missing much on a gluten-free diet. Wheat can kill. I can't see how it can be good for anyone if it can do devastating things to so many people. Birthday and pizza parties are tricky but I'll take the trickiness over having a sickly child anyday.
Good luck. I hope all my rambling helped.