Zizzle,
Wow! You're chock full of downright profound questions, today. I wish I knew the answers, but the best I can do is offer a non-professional opinion.
Zizzle wrote:Could their trip through mom's altered gut flora be to blame for all this?
Maybe. It would surely be very enlightening to see data that linked mothers with an IBD, with the the long-term status of their children's health, (i. e., whether or not they developed related GI issues, or other autoimmune issues, during their lifetimes.
Zizzle wrote:Which makes me wonder...Should people with IBDs have elective C-sections to avoid passing on their pathological mix of flora??
This answer would have to depend on the answer to the first question, but the problem is, statistics show that babies delivered by C-sections are typically worse off than those born naturally, so someone needs to figure out the correct way to safely and properly jump-start the immune system on babies delivered by C-section.
Zizzle wrote:I had mastitis 4 times while trying to breastfeed my son. Would I have been better off pumping and dumping during those periods on antibiotics?
Yes, IMO. Dairy farmers have always dumped milk from a cow being treated for mastitis. I'm not sure if that's a USDA requirement, or not, but I always assumed that it was. To be honest, I'm kind of surprised that it's not highly recommended for humans.

The point is, if USDA feels that humans of any age should not be drinking milk from a cow being treated with antibiotics, why would the FDA feel that it's OK for babies to drink milk that contains antibiotic residues?
Zizzle wrote:While I agree with all this, are Gen X perfectionist mothers going to go crazy blaming themselves and their bodies for their children's ADD/autism/allergies/IBDs, etc? When we can also agree that other environmental factors must also be at play (chemicals, pollutants, etc)?
I hope not, since they're paying for, and following the advice of medical professionals. IMO, that relieves them of any sense of responsibility. If they were acting on their own opinions, I can see how they might feel responsible, but that's not the case - they're relying on professional advice. That's why they work with an OB/GYN.
Tex