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To me, the joke here isn't that spooning with a male would be uncomfortable. The joke is that you are spooning with a colleague, in the office. It's a transgression of the relationship you have with colleagues and a transgression of the normal activities that happen in an office environment. That's what makes it uncomfortable and thus funny. That the colleague is usually male is besides the point: it is even funny to gays that feel uncomfortable when thinking about spooning with a colleague in the office.
So you are completely right that a feeling of discomfort underpins this humor. I just disagree with the source of the discomfort.