In my view, as some others have said, the "great wheel" was always just one way of looking at the multiverse. An "artistic representation," not a literal truth. All those other planes can still exist (and more!), and just not be common action on the Material Plane (they are the Clueless, after all).
What's going to bump it around more is the shakeup of the planar peoples, the demons, the devils, the celestials, the slaadi, the elemental planes, the yugoloths, the eladrin...this is going to change the conflicts in and around Sigil pretty dramatically. Not that that's totally a bad thing.
A paragraph in the DMG isn't much, but it's enough to say "Sigil is a planar metropolis where beings from other planes comingle under the watchful eye of a mysterious being called the Lady of Pain, about whom little is known with certainty. Called 'The City of Doors,' it contains portals to every other plane in existence (including alternate material planes). It is also known as 'The Cage,' because these portals are the only way into or out of the city. It is shaped like a torus, with the city on the inside of the disc, but nothing outside of it. Philosophy and politics characterize the lives of those who live here, and many claim allegience to one of several philosophical clubs, called 'Factions,' whose influence is felt in the city and beyond. Though the Lady of Pain recently officially disbanded the Factions due to a violent war, the Factions are, at their core, philosophical ideas, which are much harder to eradicate, and so have clung together as social groups. Because creatures from all other planes can converge here without fear of great physical violence (thanks to the godlike power of Lady of Pain), it is often used as a neutral meeting ground for otherwise warring groups of creatures."
This would pretty much make me happy enough. Heck, it's probably MORE detailed than it needs to be with that paragraph, but as long as all those are in place, it'll fit my 4e plans snugly.
