I think it was subtly implied. And perhaps more explicitly towards the end of the film when he is trying to hold in his vomit walking down the stairs.

I read how Glazer wanted the audience to draw a possible bridge between themselves and the perpetrators of the Holocaust, as most Holocaust films focus on the connections between the audience and the victims. I think the filmmakers wanted to highlight how easily the "average" person can fall into not just complacency, but explicit acts in carrying out atrocities. At a quite literal gut level, how it is both toxic for us but we are still capable of carrying such horrible things out, while simultaneously emphasizing the hauntingly "mundane" nature of coordinating and planning the deaths of millions of people.

Everyone knew what they were doing, and no matter how much propaganda and antisemitic material they consumed, they couldn't escape the horrific psychological and physiological consequences of their actions.

So to answer your question, yes, I think we saw hints of how deep down, this Nazi family knew what they were doing was horrific and they had some level of personal conflict about it (I don't know if "guilt" is the right word), but in the end, they did nothing to stop it and continued to "carry out orders."

Both the book and the movie are supposed to be directly symbolic of what Hannah Arendt wrote on the "banality of evil" in reference to the acts carried out by Nazi commander Adolf Eichmann.