What is the grammatical number of an inline citation? Which of the following is correct?

a) Johnson et al. (2010) prove that all snow is yellow.
b) Johnson et al. (2010) proves that all snow is yellow.

I suppose the question boils down to whether I'm citing the authors or their paper. If the paper is the subject of the sentence, it's singular (b). If the authors are the subject, then it's plural (a).
I personally am comfortable with both ways, for exactly the reasons that you give: it's entirely reasonable to refer to either the authors or the paper.  The important thing is to be consistent with your usage throughout a manuscript, else your readers may wonder why you feel it appropriate to refer to some authors directly but not others.