Megan, if it were me, I'd look for a new GI. It sounds like your current GI is being very dismissive of your symptoms. And IBS is typically a diagnosis of exclusion, meaning they've ruled out every other possibility - and it sure sounds to me like they haven't, if they haven't looked at your small intestine at all. You're not a hypochondriac, don't let your doctor make you feel that way. Sometimes doctors are too lazy or just want to put a label on something, so they call it IBS even when that doesn't seem right. You know your body best and you know that something more than "just IBS" is going on, so don't stop fighting. I know you're tired and frustrated, and it's okay to give up for a little while, but after that you know you need to pick up the fight again and keep looking for proper answers. I feel for you, because I've been there & done that for 7 years and counting. It's incredibly exhausting and endlessly frustrating, but we're here for you. Don't give up. Ask your PCP for a referral to a new, better GI. Your PCP might know of a good one, if not, check with your insurance company to see which GIs are covered under your plan, then do some googling and look at the doctor reviews here on the forum to see which ones sound the best to you.
Here's the link to the forum's doctor directory and doctor reviews:
http://www.crohnsforum.com/doctor/
http://www.crohnsforum.com/forumdisplay.php?f=79
As for B12 deficiency - it's extremely common in Crohn's. B12 is absorbed in the terminal ileum, which is the last part of the small intestine, and that's the spot where Crohn's most commonly manifests. If the terminal ileum is inflamed or has scar tissue, then it's not able to absorb B12 as well as healthy tissue would, and as a result, a deficiency occurs. So look for a new GI, and ask them to check out your small intestine. That's what I would do.