When lever is in on-state and I use command block to replace it with off-state lever, redstone state remains on.
/setblock ~ ~ ~-2 lever 3
If I use two command blocs and first remove lever and then add new off-state lever, everything works fine.
/setblock ~ ~ ~-3 air
/setblock ~ ~ ~-2 lever 3
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Confirmed for 14w21b

Is this still a concern in the current Minecraft version? If so, please update the affected versions in order to best aid Mojang ensuring bugs are still valid in the latest releases/pre-releases. If this has been done, we can reopen the issue.
Keep in mind that the "Resolved"-Status on this ticket just means "Answered", and that we are waiting for further information on whether this issue still exists or not. We will reopen it as soon as the requested information has been delivered.
Confirmed for 14w08a