I also has the problem with the thinkfinger. I don't access the libgksu source 
codes so I don't know what happened in it.
I almost start to modify the thinkfinger source codes.
What I plan is to add a dbus server to listen it and modify the promote codes 
in pam_thinkfinger.c to call dbus method. Then the server may popup a hint 
dialog to ask user to scan his fingerprint.
Fortunately I search it in launchpad.
Now what I'm understanding is gksu will parse the input from sudo's output 
through the wrap pipe.  While the PAM module invoke sudo, it doesn't pass the 
PROMPT as sudo -p PROMPT, so gksu cannot get anything and it will think it's 
unnecessary to ask for password? 
But the PAM module will make sudo to input the words they set in their codes. 
So it's not possible for gksu to adapt all kinds of output. 

In my opinion it's not only gksu's fault, of course it's not sudo's fault.
Currently I can't find gksu's source codes. But I think it's kind of 
inter-process problem. It will be better for gksu to know when sudo will ask 
for passwords instead of reading the sudo's output.

I think a temporary method is to grab all output from sudo and display
to user until sudo exit.

A long term method is to change PAM module to enable something like hook
or notifier to allow user to customize their modules interfaces instead
of command line only.

Do you think it's ok to add a dbus support in the thinkfinger? After reading 
the bug, I'm considering if it's worth doing it.
I'm glad to help to do something if needed. Currently I can only modify the 
thinkfinger's prompt to "Password:", sigh.

-- 
gksudo fails if using libpam-krb5 for password auth
https://bugs.launchpad.net/bugs/15093
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