Since the article uses evolution metaphors, how about this: forks can be a good way to help organisms (read: projects) navigate a complex multivariate fitness landscape. Abandoned forks then serve as concrete markers of particular design decisions that can be revisited later if a similar kind of problem comes up.

We often don't know ahead of time how a decision will work out, so calling these forks "wasted effort" seems to miss their utility as experiments that can drive the direction of future development indirectly.