If you disable JS in all browsers, IE9, Firefox, Chrome and Opera render the page the same. This leads me to believe the web designer is writing brittle javascript somewhere. If you look at the JS, is uses conditional comments based on the version of JS, so I would probably start looking there.
In the end I don't think we can expect to push the web development field and browsers forward without dropping old cruft. From using IE9, it seems they've made a big jump with this version. Unfortunately some old code may no longer work the same, and for that there is the X-UA-Compatible meta tag.
Let me answer this as someone who writes non-brittle Javascript code on a 1 year old web app (e.g. I have more unit tests per LOC in my Javascript than most of the Java code that's in the underlying app. AND I run my test suite on all major browsers regularly).
Even if you write solid code, using good architecture, and thorough testing you will find that if it passes on FF then there's a 98% chance it also passes on Chrome and Opera... but maybe a 60% chance that it passes on IE8 (requiring HOURS of work to investigate and fix), and there's some abysmally low rate of success on IE9 from having run these tests against the Beta earlier (we don't plan to announce IE9 support for a while).
So while you are correct old cruft will have to go, brand new solid code shouldn't have to go as well... and that's unfortunately the consequence of IE9. :'-(
In the end I don't think we can expect to push the web development field and browsers forward without dropping old cruft. From using IE9, it seems they've made a big jump with this version. Unfortunately some old code may no longer work the same, and for that there is the X-UA-Compatible meta tag.