It's just the way his ult is designed. There's no way to reduce this weakness without reworking him.
What they could (and to be honest, SHOULD) do is bring the cooldown of his E back to 3 seconds (bringing it to 4 did a lot of terrible horrible things...as well as ruin the overall flow of his entire kit) or give him slightly more damage on his Q. Or make his ult do up-front damage that isn't part of the pop damage. Or, during the amount of time it takes to reach his target during his ult, if they became untargetable during this time then Zed's ult will only go on a 5 second cooldown. But if they Zhonya'd after he lands, he still suffers the full cooldown (but he still is able to deal a split second worth of damage, like an autoattack + E). Or some kind of combination of these things.