I would argue that the answer to both of these questions is “yes.” There is a way to claim that Yoder is consistent with communitarian ideals and there is a way to claim that this is counterintuitive. It is counterintuitive to use communitarian ideas to defend a decision that allows part of the community to reject the values of the larger community as a whole.
Communitarian ideals emphasize that there should be a strong tie between the members of a community. The people of the community should not focus too strongly on their individual rights. Instead, they should subordinate individual desires to the needs of the whole community. We can say that this is what the Court is allowing with its decision in Yoder. It is saying that the Amish community has the right to maintain its community values. It has the right to keep its community the way it wants it. Therefore, it has the right to say that children will not continue to go to school after 8th grade. In this way, we can say that the Court made an exception that was consistent with communitarianism.
Now we ask whether this is counterintuitive. I would argue that it is. This decision sets a precedent that allows the Amish community to maintain its own ways. This is communitarian. However, at the same time, it goes against the communitarian interests of the entire society. It is allowing the Amish community to essentially withdraw from the larger society. In this way, the decision is simultaneously upholding the ideals of communitarianism for a small community (the Amish) while going against them for the larger community as a whole. This is counterintuitive.