What happens to the maximun operating ratings when the device is unpowered?
You are right, when the circuit is unpowered the CT output could violate the absolute maximum ratings of the opamp.  This is not good.

The protection diodes will be forward biased, and the power rail partially powered.  This might be OK, depending on what is connected to the opamp power and what exactly the datasheet says about this.  It might be acceptable to add diodes in series with the opamp power leads so that the &plusmn;1 V on the input pins doesn't try to power up the whole power net.  If you do this, make sure to put the bypass capacitors on the opamp side of the diodes.

However, a simple fix is to use a CT with half the gain.  Now it will produce only &plusmn;500 mV signals, which the opamp can handle when powered down.  You've got a amplifier in there anyway, so &plusmn;500 mV should be good enough unless you're doing something unusual.