I think it sounds like a great opportunity. I did something similar a few years ago (OK almost 10 actually). I was working as the assistant MIS manager for a large company with a long established history. The salary was good, the benefits were great, 401K plan was very good... but the work was mostly unrewarding and the demands were ever increasing. However, none of the downside would have mattered that much if it weren't for all of the corporate politics.
I took a position initially as an outside consultant and later as an FTE with a
much smaller company (former company had >3500 employees... new company had 22). Starting salary was less than 60% and no 401K, benefits were crap, etc... but I had complete autonomy and could pick my projects and was given a moderate profit-sharing agreement moving forward.
My workload still sucks (60+ hrs/week) - but after initiating several successful projects and managing a couple I'm now much, much better compensated (~10X my starting salary) - and other than the occasional heated discussion with the owner over company direction... there's zero politics and I'm much happier!
So, although the initial hit might seem a little daunting - I personally will never consider the 'stability' of the big corporate structure to be anything other than a potential nightmare waiting to happen. You can't afford as much complacency at a smaller company - but you can also see much greater rewards for hard work and dedication!
Good luck with whatever you decide. It sounds like you're going to come out of this just fine no matter what.
