Great! Inserting zeroLevelTol=>1E-15 in my pgml answer checker did succeed both in preventing a response of 0 to be marked correct and also in displaying the correct nonzero answer.
It did not change the fact that the student's correct input is still shown as 0 (and the student's answer preview still shows the full input). I can live with that.
In a part of my exercise which I did not post here, I had students fill in a table with a few more values (radii of other elements) of order 10^-(13). The table was not in the pgml section (I have yet succeeded in getting tables in pgml), and I was not successful in getting the zeroLevelTol=>1E-15 to affect the display of the correct answer for those, only to display 0.
But I'm not planning to solve that puzzle, instead I've decided to ask for the table values to be input in units of 10^(-13), and everything seems to be working fine.