1) The video talks about forking code, pair-programming with spooning, and knifing (pull requests): fork, spoon, and knife. I just wondered if they have a chopsticks version, for people who prefer using chopsticks.
2) Then I realized there is already a context that involves pairing and chopsticks: Chopsticks is a common piano duet. Of course, it doesn't have to be played by two people...
(The video begins with the version you typically hear kids playing, but then, well, you have to watch!)
: Yes, I read that article on sexism the other week… call me insensitive, but I think lighten up is a perfectly valid answer in this case.
Stop it! You guys are killing me!
As a bisexual spooning enthusiast and also a developer, I personally don't mind; I think it's totally valid, and potentially pretty funny, to feel apprehensive about that kind of thing. I understand that feeling because that's how I feel about paired programming much of the time ;)
 The connection to bigotry comes from the notion that bigotry against gays is motivated by the psychological fear that gays will try to have sex with you; hence someone who seeks to oppress gay people is motivated by homophobia in the more literal sense. No comment on the validity of that notion.
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.
It's not a stereotype; the whole point of literal homophobia is that male-male intimacy does border uncomfortably on the homosexual.
In any case, your interpretation of the joke is probably more on target; I was just explaining how it could be seen as homophobic.