I'd say they ought to suck up whatever embarrassment they may have over not taking communion, and just not take communion, and accept a blessing from the Priest, or leave it be altogether and just stay in the pew during this time. This is for survival of not only the soul, but even one's earthly body. (Although an Atheist wouldn't believe in a soul or hell or damnation or sickness or death by supernatural means, so it's unclear why they are in a Eucharistic setting to begin with).
This is St. Paul's warning about it. And this was presented to believers!!
23 The tradition which I received from the Lord, and handed on to you, is that the Lord Jesus, on the night when he was being betrayed, took bread,24 and gave thanks, and broke it, and said, Take, eat; this is my body, given up for you. Do this for a commemoration of me.[6] 25 And so with the cup, when supper was ended, This cup, he said, is the new testament, in my blood. Do this, whenever you drink it, for a commemoration of me. 26 So it is the Lord’s death that you are heralding, whenever you eat this bread and drink this cup, until he comes. 27 And therefore, if anyone eats this bread or drinks this cup of the Lord unworthily, he will be held to account for the Lord’s body and blood. 28 A man must examine himself first, and then eat of that bread and drink of that cup; 29 he is eating and drinking damnation to himself if he eats and drinks unworthily, not recognizing the Lord’s body for what it is.[7]30 That is why many of your number want strength and health, and not a few have died.[8] 31 If we recognized our own fault, we should not incur these judgements;