It seems like we should be accounting somehow for the total number of papers published in a field.  Assuming that a constant level of "disruptive science" occurs per year, then more published papers would lead to less average disruptiveness. So, rather than measuring disruptiveness per paper maybe we should be looking at disruptiveness per year or even per worker-year. 

While this might well be true, my immediate thought is to ask whether the measure of "disruptive" increases over time for any given paper after it was published, and my second thought (on finding it's based on citation patterns) is to ask whether changes in citation methods/fashions over time might spuriously affect this measure. 

And:

The authors reasoned that if a study was highly disruptive, subsequent research would be less likely to cite the study’s references, and instead would cite the study itself. Using the citation data from 45 million manuscripts and 3.9 million patents, the researchers calculated a measure of disruptiveness, called the CD index, in which values ranged from –1 for the least disruptive work to 1 for the most disruptive.

wouldn't that tend to increase over time for any given paper?