Just a few notes, and then I'll stop beating what's starting to feel like a dead horse (on my part, that is. Everyone else's perspectives have been *incredibly* useful, and I thank you for your insights).
We definitely didn't linger after we were asked to clear the table. We were taken aback, no question, so there were a few beats while we gathered our wits about us and figured out how to proceed gracefully. And of course there's the time required to figure out the tip, divide the check, gather our coats, etc. But once asked, we were essentially on our way.
If I'm being honest, I think the reason this incident bothered me is that it's embarrassing. A good meal, particularly one that takes its time, creates a kind of intimacy between restaurant and guest. (NeroW, you may be exactly right that they were pacing the meal in what they may have perceived from us. For my experience, though, it felt more like we were adapting to the kitchen's pacing, which felt wonderfully gradual after a week nothing short of a pressure cooker). When an incident like this happens, it damages that intimacy, putting some fairly cold distance between all parties, and even potentially between the dining companions themselves. You're absolutely right: It is just dinner, and I'm probably being a little grandiose with my metaphors, but it really did feel like a cold bucket of water tossed on an otherwise warm experience.
One other reason, I think, for my surprise is that when I called for the reservation, I was told we had a choice between 6pm or before, or 9pm or after. I took the 6pm, and I suspect this put in my mind the idea that they have two seatings a night, one at 6 and one at 9. I was very conscious of not staying beyond a time that would have allowed them to clear our table and make way for the 9pm seating. But we were asked to leave much earlier than that (as a point of reference, I live about 1.5 miles from the restaurant, walked my friend to the bus, biked home in the flurries, and was home before 9pm).
It sounds to me, once accounting for all vantage points, that we were probably just on the cusp of staying too long for our party size and menu. But since it wasn't egregious -- and since we were quiet, respectful, appreciative guests -- I'd like to hope that a server would find a more graceful way to encourage the transition.