Gary I hate to say it, but I think the problem here is that you assumed the town's building inspectors would protect you, and frankly, that's not what they are there for. They are codes enforcement folks, and the codes they enforce are the ones the township passes; codes like new construction requires an electrical inspection inspected by a licensed electrician, ditto on plumbing; ditto on hvac, etc. As for overall architecture and engineering of the house, that's not their job. They can do their job 100% correctly and have everything meet local codes, and the house can still fall into the basement.
Also, I know the tri-state area, having lived there for 10 years, and I think I know CT pretty well. There are a LOT of small builder and shaddy contractors, and worksmanship and doing things right are NOT high on the list for many of these folks. I bought a 70yo house in Westchester Co, NY in '91 and I wouldn't have dreamed of buying it or anything in that area without both a lawyer AND a building engineer. When I bought that home in '91 the cost of the lawyer and the engineer TOGETHER was less than $1000.
Sorry for the salt on the wound, but I fear that this is probably going to end up as a costly life lesson.
Now, with all that said, ask your builder to think OUTSIDE the box....would seem to me that even if you have to put beams and pillars out in the open, in the middle of ceilings and rooms that isn't THAT BAD an option IF it means the house becomes safe and you save 100s of thousands of dollars.
TJR