I've managed to create a (relatively) minimal reproducer. Download my guest config tarball from here:
http://people.redhat.com/mbooth/tmp/rhel54pv64-config.tar.xz

Expand the tarball, then run:

$ augtool -r root
augtool> defnode new "/files/boot/grub/menu.lst/title[last()+1]" "Red Hat Enterprise Linux Server (2.6.18-128.el5)"
augtool> save
Saved 1 file(s)

At this point, without closing augtool, independently edit root/boot/grub/grub.conf with a text editor. Remove the first grub stanza[1]. This corresponds to the behaviour of rpm -e kernel...

augtool> load
augtool> save
Segmentation fault (core dumped)

Although the above only touches files under /boot, when I tried this without any files under /etc it didn't crash.

Matt

[1] For clarity, this will leave the following:
# grub.conf generated by anaconda
#
# Note that you do not have to rerun grub after making changes to this file
# NOTICE:  You have a /boot partition.  This means that
#          all kernel and initrd paths are relative to /boot/, eg.
#          root (hd0,0)
#          kernel /vmlinuz-version ro root=/dev/VolGroup00/LogVol00
#          initrd /initrd-version.img
#boot=/dev/xvda
default=0
timeout=5
splashimage=(hd0,0)/grub/splash.xpm.gz
hiddenmenu
title Red Hat Enterprise Linux Server (2.6.18-128.el5)

--
Matthew Booth, RHCA, RHCSS
Red Hat Engineering, Virtualisation Team

GPG ID:  D33C3490
GPG FPR: 3733 612D 2D05 5458 8A8A 1600 3441 EA19 D33C 3490

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