Yes, I’m positive they’ve learned from past mistakes. This already shows in actions taken (and described above). However I give you that there might be new traps to fall in. It’s the future we are talking about after all
IMHO these are two different issues and not to be confused. Let me explain by first going into details why including GApps out of the box is important and then elaborate why Fairphone still doesn’t restrict our freedom any more by doing so.
Fairphone is trying to sell 100k+ phones a year (which I think is a good thing). Regular customers expect certain features of phones. Having access to the Play Store and other Google Services are among these features. And, frankly, although we really love free and open software, we all know that there are no equal open alternatives with the same level of quality, security, etc (I’m talking mostly about the Play Store here).
This means that if Fairphone wants to appeal to a larger market and promote their ideals (that you probably share as I do) to a large audience, they need to offer a great out of the box experience. Including Google Services without any shady workarounds is a step in that direction. Hence there are plenty of reasons to include GApps when shipping Fairphone 2.
At the same time Fairphone is actively trying to rectify many of the issues experienced with edition one by choosing a platform that makes it possible to develop and use alternative ROMs and OSs, proactively talking to other OS vendors and providing source code ahead of time. That means they are both trying to give us options and empowering us to create our own alternatives. I hope/expect that Ubuntu/Sailfish/Cyanogenmod will be much easier to port to Fairphone 2 than compared to FP1.
By providing this combination of options (GApps by default but alternatives readily available) Fairphone gives us the best of both worlds.