The .gvfs is created by GVfs under GNOME. Looking at the Wikipedia page, you can find that GVfs (abbreviation for GNOME Virtual file system) is GNOME's userspace virtual filesystem designed to work with the I/O abstraction of GIO.
The most probable situation concerning your problem is that some Gnome program still runs in the background with the user id of the user you want to delete. I experienced the same problem as well.
The solution is to kill all programs associated with that user id. From the shell you can check whether some program is running with that user id before terminating them by typing
ps -U username
You can terminate (kill) those programs by using the command always from the shell
sudo pkill -u USERID
where you can find the user id for instance by
id -u username
Afterwards, it should be possible to remove the user home directory by
rm -r /home/username