Personally I'd rather regenerate the world from scratch and embark in the same spot with the intended embark size.
While that's easy enough (if you don't hit one of the worldgen aspects that don't strictly the follow the same result from the same Seed, which might not happen these days and I don't think ever effected geography/geology anyway) I personally I always (
always) go in and make a copy of a freshly worldgenned save (by personal tradition, "region1"->"region1.orig" before I open it as an wctive game. It saves me the effort (mostly time) of recreating an embark opportunity if my very first striking of the earth leaves me with a scenario that doesn't sufficiently match what I had started to expect and I wish I'd not chosen it/shifted another tile into or out of the steep-sided hillside above the floorplane/whatever...
(I may also duplicate it
again to run a parallel Adventurer on the world, of course with only shared prehistory, not in any way to interact fort and adventurer (or the remains of one or the other). It's just a thing I do.)
Not really a post-hoc solution to the original issue, nor do I really consider it save-scumming (I have Seasonal Saves for that, though if I use them at all it's mostly for forking an abbreviated redo of a cistern dig/whatever, just to see if I could have done it better, and consider my main save still the true one), but it's a cheap and easy way of overcoming OP's problem, and various other issues, if you make it an option in advance. If you're not put off by the whole redo-from-start.
Other than this, I've had not much to add to this thread as I saw it develop (retire and (over)reclaim the structures was my first thought, and take your chances with the rest), except that I also tend to have no-wood goods grouped handily without wood 'contaminents' in stockpiles that might go to trade, and (another personal foible, here) as I never sell
any bin, just the contents (a net inflow of bins by buying bins of leather, etc) then I'm never in danger of accidentally contaminating the stone crafts with their wooden bin container (if so it is, which it usually is).
So just "go back in time and do it differently" is my solution, I know, but you might find it something worth thinking about in future circumstances. Or not.