Of course, ++ Cupich doesn't really believe this: “If people come to a decision in good conscience then our job is to help them move forward and to respect that. The conscience is inviolable and we have to respect that when they make decisions, and I’ve always done that.”
If, for example, someone arrived at a decision 'in good conscience' to start a branch of the Ku Klux Klan in his diocese, and start lynching black people, and still presented for Holy Communion, I suspect he would have something to say about the matter. Or if I, in good conscience, were to seize the microphone from him in his Cathedral, and declare that I believed he was in grave error, and further made it clear that my conscience compelled me to do so every time he celebrated Mass publicly, then again, I suspect he would struggle to respect that decision and help me to move forward with it.
One could push the argument further (and indeed many have done so); what about the paedophile or the rapist who has convinced himself that his behaviour is allowable in good conscience? For the capacity for human self-deception is enormous, not least when one's mind and judgement are corrupted by habitual serious sin.
His argument, I imagine would be that one could not arrive at such decisions 'in good conscience.' Which is reasonable enough. But that then begs the question about how one discerns (and who discerns) what decisions are made in good conscience - not least ones that fly in the face of the teaching of the Church which he has devoted his life (one assumes) to proclaiming and upholding.
What this kind of statement really means, in practice, is that the speaker respects decisions with which he does not fundamentally disagree. And it is a sorry story if an Archbishop does not fundamentally disagree with decisions to continue in sin.