It never even would have occurred to me to interpret this as an insult the shipper fans--if anything, it's a wink at them. The romance in GG is conscious and perfectly under the control of the authors, which is especially clear when they do meta commentary on it.
The Foglios have been surviving at the fringes of comics publishing for a long time; they earn a considerable portion of their income selling their work directly to their fans. They navigate the creator/audience relationship with grace and savvy, and I've yet to see their fans respond to them in any other way.