I don't know that the user names are supposed to dissappear from these files. How are you doing the kill for the user?
kill ${PID} or kill -15 ${PID}?
If so, this may or may not kill the user out of the system, I have had very little success with killing users out using the above examples. I have always had to use the following:
kill -9 ${PID}
The names stay in utmp and wtmp, but they do not show up in who. I would say that if the name is still showing up in who, then the user is still logged in and you need to force the kill with "-9".