Pope Francis' revision of the Catechism does not contradict John Paul II's thinking on this issue, especially as seen in the encyclical Evangelium Vitae. Francis' revision is just finishing the work that John Paul II began regarding capital punishment. Therefore Francis has not 'trumped' Evangelium Vitae.

Pope John Paul II

First, let's have another look at section 56 while emphasizing a different side of the story with bold text:

On this matter there is a growing tendency, both in the Church and in civil society, to demand that it be applied in a very limited way or even that it be abolished completely. The problem must be viewed in the context of a system of penal justice ever more in line with human dignity and thus, in the end, with God's plan for man and society. [...] (EV 56).

It is clear that, for these purposes to be achieved, the nature and extent of the punishment must be carefully evaluated and decided upon, and ought not go to the extreme of executing the offender except in cases of absolute necessity: in other words, when it would not be possible otherwise to defend society. Today however, as a result of steady improvements in the organization of the penal system, such cases are very rare, if not practically non-existent.

In any event, the principle set forth in the new Catechism of the Catholic Church remains valid: "If bloodless means are sufficient to defend human lives against an aggressor and to protect public order and the safety of persons, public authority must limit itself to such means, because they better correspond to the concrete conditions of the common good and are more in conformity to the dignity of the human person".[48]

-Evangelium Vitae, 56

John Paul II's thought on this issue moved the Church in the direction of abolition by way of human dignity, and this is exactly what we see in section 56.

Safeguarding the Death Penalty?

The key question which concerns us is this: Did John Paul II intend to safeguard the death penalty in Evangelium Vitae? Of course everyone knows that he wanted to severely limit the practical application of capital punishement, but did he also want to safeguard the possibility of the practice? Only if he intended to safeguard it would there be a tension between John Paul II's teaching and Francis' teaching.

There are two reasons why I don't see evidence of this. First, his reasons given for limiting capital punishment reflect an understanding which sees the death penalty as justified only "when it would not be possible otherwise to defend society" (EV 56). Thus he saw capital punishment as a necessary evil that ought to be dispensed with as soon as possible. Nowhere in Evangelium Vitae do we find the claim that capital punishment cannot be abolished. On the contrary, we read that the cases where capital punishment can be legitimately applied "are very rare, if not practically non-existent," and that "If bloodless means are sufficient," then they must be used.

The second reason is weaker. It is that his teaching on capital punishment caused wariness among conservative theologians who affirmed the Church's long practice of allowing capital punishment, such as Avery Cardinal Dulles. Such theologians were relieved when then-Prefect of the CDF, Joseph Cardinal Ratzinger, wrote a letter to Cardinal McCarrick. The third section of that letter informs us that Catholics may disagree with the Holy Father on the matter of capital punishment. The conservative theologians were worried about an abolition of the death penalty, and their fears were not assuaged by the writings of John Paul II.

Francis

Pope Francis' revision to the Catechism makes use of arguments which are very similar to Evangelium Vitae (e.g. a focus on safeguarding society, emphasizing modern prison systems capable of carrying out life sentences, and a very similar theory of punishment). Like John Paul II, he relies heavily on the idea of human dignity, even using it as the centerpiece of his conclusion, "the death penalty is inadmissible because it is an attack on the inviolability and dignity of the person" (This quote is included in the draft for the Catechism revision and originally comes from this address).

John Paul II said, "If bloodless means are sufficient to defend human lives against an aggressor and to protect public order and the safety of persons, public authority must limit itself to such means..." (EV 56).

Francis has essentially said: Bloodless means are sufficient, therefore the death penalty is inadmissible. John Paul II wrote the conditional; Francis affirmed the antecedent. We all know what follows. "Trumping" only comes into play when there are opposing views. It doesn't apply here.

(It should be noted that while I personally disagree with Francis' revision, I obviously do not believe that it is inherently contrary to John Paul II's teaching on this subject.)