Jean, in her "strongest form"(which is her most balanced one), is White Phoenix of the Crown. The same Phoenix who held the entire universe in her hand and altered the whole time stream without so much as breaking a sweat.
Furthermore, Jean can't die. No matter how many times he will kill her - she will always come back, she's a manifestation of the Phoenix Force - and as long as the force exists - so does she.
Now, let's go a step further. Superman, no matter what he does(sorry but I really am clueless about Superman Prime) - can't destroy a force of creation, simply because it is a Force. The Phoenix force is the sum and substance of all that lives. Its cosmic energy not only represents all current life, but also future generations. He can't destroy a force.
And let's go another step ahead. Let's say he does manage to kill the force. If the force is destroyed - all life in the whole multiverse will end, meaning that he too will die.