Stated more precisely: a non-GPL-compatible license for an extension means that the extension can never be distributed with core.
The idea that deployment of software on a server entails license obligations is a GPLv3 feature; mediawiki is licensed under the GPL v2 ("or later" for theoretical redistribution purposes).
Presumably deployment of a GPLv3-only or [[Affero GPL]] extension on a WMF server might be more problematic, iff WMF were deploying non-GPL-compatible extensions (I don't know whether that's the case one way or another). But that's rather orthogonal to the "openness" of the source.
Anyway, we could devolve into a flame war and/or "discussion" of the merits and disadvantages of various software licenses rather easily, so I'm suggesting that we limit further discussion on this thread absent a more focused question from Jeroen. --scott