I've come across the same issue in a homebrew world I've been trying to port over from 3e to 4e. Initially I had antimagic as a significant part of the world's setting, and why certain things worked the way they did. But it's prohibitively difficult to implement antimagic without severely unbalancing the classes. I think I'm going to end up just scrapping the idea and saying magic works everywhere now.
One thing that's occurred to me--assuming no multiclassing and no martial-esque feats, a pure wizard is probably actually less nerfed by antimagic in 4e than in 3e. A pure wizard in 3e is left with nothing but not-even-all-simple-weapons, and a BAB that falls further and further behind fighters the higher you go (and antimagic's usually pretty high up.)
4e, all your powers are nerfed except basic physical attacks and second wind, but at least you keep your 1/2 level to everything, which is the same 1/2 level that the fighter gets. Your strength will be lower, granted, but it's not as huge a delta as the old 1/2 BAB versus 1 BAB issue.
The thing is, 4e is designed with much tighter balance than 3e, so although nerfing magic for an encounter would be a nuisance to a wizard in 3e ("sigh, i guess i suck this encounter"), it's almost unprecedented in 4e because so very few things generate the "you suck this encounter" effect.