I need to make two datasets commensurate. Can I "commensurate" them?
According to the OED, you can. It lists a transitive definition of commensurate with a citation in 1655. If you wish to "proportion, or make to correspond in nature", then this is your word.
Just because this use of commensurate appears in the OED, don't feel compelled to adopt it, however.
The Ngram viewer shows a frequency of 0.000001% for the infinitive "to commensurate" - not an altogether fair snapshot, but enough to suggest that one uses the word as a verb at the peril of having it questioned here on EL&U or by even higher authorities.