Did you try deleting the w3af folder? I remember having to do that to fix this.
apt-get remove w3af
rm -rf /pentest/web/w3af
apt-get install w3af
Here is the error I get before doing this
I remember on another instance getting the error you got and this is how I fixed it then as well
Failed to get an instance of "gtkOutput". Original exception: "HistoryItem instance has no attribute 'initStructure'".Traceback for this error: Traceback (most recent call last):
File "/pentest/web/w3af/core/controllers/misc/factory.py", line 60, in factory
res = aClass(*args)
File "/pentest/web/w3af/plugins/output/gtkOutput.py", line 88, in __init__
AttributeError: HistoryItem instance has no attribute 'initStructure'