Another work-around, though not ideal, is to install an older version of XQuartz. I finally did it this morning after being fed-up with the weird AFNI behavior (i.e. crash after closing a sub-window, etc).
Here is what I have:
OS X Yosemite v10.10.5
XQuartz 2.7.7
Note, this might have consequences for other software but I haven't run into anything yet.