How to test from Honza:

$ ipa user-add root --first Fake --last Root --sshpubkey="`cat .ssh/id_rsa.pub`"
...
  UID: 1192200011
...

$ ssh root@localhost
Last login: Mon Dec 10 04:46:42 2012 from somewhere.example.com
# id
uid=0(root) gid=0(root) groups=0(root)

To amend the How To Test..what I wrote in comment #1 was the "before patch" behaviour. After the SSSD is patched, then you shouldn't be able to log in with your public key.

I still see the "before patch" behaviour, able to login with public key.

[root@rhel64master ~]# ipa user-find --login=root
--------------
1 user matched
--------------
  User login: root
  First name: Fake
  Last name: Root
  Home directory: /home/root
  Login shell: /bin/sh
  Email address: root
  UID: 1114200003
  GID: 1114200003
  Account disabled: False
  Password: False
  Kerberos keys available: False
  SSH public key fingerprint: E0:25:07:C3:96:93:75:F8:1D:05:C2:95:A7:1C:22:BD root@localhost (ssh-rsa)
----------------------------
Number of entries returned 1
----------------------------
[root@rhel64master ~]# ssh root@localhost
Last login: Thu Jan 31 00:49:12 2013 from localhost
[root@rhel64master ~]# id
uid=0(root) gid=0(root) groups=0(root) context=unconfined_u:unconfined_r:unconfined_t:s0-s0:c0.c1023
[root@rhel64master ~]# logout
Connection to localhost closed.
[root@rhel64master ~]# 
[root@rhel64master ~]# rpm -q sssd ipa-server
sssd-1.9.2-82.el6.x86_64
ipa-server-3.0.0-24.el6.x86_64
[root@rhel64master ~]#

That's because you authenticated by some other means (either GSSAPI or public key authentication with a key found in an authorized_keys file).

Make sure the file /root/.ssh/authorized_keys does not exist on rhel64master and either run kdestroy before running ssh or run ssh with "-o GSSAPIAuthentication=no".

You can check that SSSD is in fact not offering sshd any public keys for root by running "sss_ssh_authorizedkeys root".

Verified.

sssd and ipa-server version:
============================
[root@rhel64master ~]# rpm -q sssd ipa-server
sssd-1.9.2-82.el6.x86_64
ipa-server-3.0.0-25.el6.x86_64
[root@rhel64master ~]#

I realized that it was authenticated by public key authentication as key was existing in /root/.ssh/authorized_keys

Installation scripts was copying that key.

cp /root/.ssh/id_rsa.pub /root/.ssh/authorized_keys
cp /root/.ssh/id_dsa.pub /root/.ssh/authorized_keys2
cp -f ./id_rsa_global.pub /dev/shm/.
cp -f ./id_rsa_global /dev/shm/.
cp -f ./known_hosts /dev/shm/.
chmod 755 /dev/shm/*.sh
chmod 600 /root/.ssh
chmod 600 /root/.ssh/id*
chmod 600 /root/.ssh/authorized_keys
chmod 600 /root/.ssh/authorized_keys2
./runtest.sh

::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::
:: [   LOG    ] :: list files in /dev/shm
:::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::

Now tried after installing ipa-server manually and removed authorized_keys, root SSH public key authentication is not successfull now.

[root@rhel64master ~]# ipa user-add root --first Fake --last Root --sshpubkey="`cat .ssh/id_rsa.pub`"
-----------------
Added user "root"
-----------------
  User login: root
  First name: Fake
  Last name: Root
  Full name: Fake Root
  Display name: Fake Root
  Initials: FR
  Home directory: /home/root
  GECOS field: Fake Root
  Login shell: /bin/sh
  Kerberos principal: root
  Email address: root
  UID: 1165000001
  GID: 1165000001
  SSH public key: ssh-rsa
                  AAAAB3NzaC1yc2EAAAABIwAAAQEAx0Hg3CZIzizMIohZydE5+cSgIyByWmD0r/J5+k2P0AveG4i5lVFhcuMasK6VYBKSrFxSgpgkw5M82Ven2lyDpFoPbPJFE8KW6eLoRPCYPO+BBaI2j9t90HueoT2y1NBrKo0QTk5fCSSGN3kKuMUCgcqQw/9ea39dFAI96szAVfk+Y1eg1E84iOg1a/usFft0r+UuOd6bxzu/1lDHo522tIhiQCKAAyxOGij3w6Zw4mfFu/99l3LKm+ACAFpeAWkJqCjfku2WIkE1qo4+lU+8SIKpFkhJIjl9JnG/9ecuMWAhiZq9Ny4lypXogbVOPZThd2nAP3x+//t7+Vrq+VXjCQ==
                  root.sjc.redhat.com
  Password: False
  Kerberos keys available: False
  SSH public key fingerprint: E0:25:07:C3:96:93:75:F8:1D:05:C2:95:A7:1C:22:BD root.sjc.redhat.com (ssh-rsa)
[root@rhel64master ~]# ssh root@localhost
root@localhost's password: 

[root@rhel64master ~]#

Beaker execution log:
=====================
Be sure to back up the CA certificate stored in /root/cacert.p12
This file is required to create replicas. The password for this
file is the Directory Manager password
:: [   PASS   ] :: Running 'ipa-server-install --setup-dns --forwarder=10.14.63.12 --hostname=dell-pe1955-01.testrelm.com -r TESTRELM.COM -p Secret123 -P Secret123 -a Secret123 -U'
:: [   PASS   ] :: Running 'rm -rf /root/.ssh/auth*'
Password for admin: 
:: [   PASS   ] :: Running 'echo Secret123|kinit admin'
-----------------
Added user "root"
-----------------
  User login: root
  First name: Fake
  Last name: Root
  Full name: Fake Root
  Display name: Fake Root
  Initials: FR
  Home directory: /home/root
  GECOS field: Fake Root
  Login shell: /bin/sh
  Kerberos principal: root
  Email address: root
  UID: 481200001
  GID: 481200001
  SSH public key: ssh-rsa AAAAB3NzaC1yc2EAAAABIwAAAQEAx0Hg3CZIzizMIohZydE5+cSgIyByWmD0r/J5+k2P0AveG4i5lVFhcuMasK6VYBKSrFxSgpgkw5M82Ven2lyDpFoPbPJFE8KW6eLoRPCYPO+BBaI2j9t90HueoT2y1NBrKo0QTk5fCSSGN3kKuMUCgcqQw/9ea39dFAI96szAVfk+Y1eg1E84iOg1a/usFft0r+UuOd6bxzu/1lDHo522tIhiQCKAAyxOGij3w6Zw4mfFu/99l3LKm+ACAFpeAWkJqCjfku2WIkE1qo4+lU+8SIKpFkhJIjl9JnG/9ecuMWAhiZq9Ny4lypXogbVOPZThd2nAP3x+//t7+Vrq+VXjCQ== root@localhost
  Password: False
  Kerberos keys available: False
  SSH public key fingerprint: E0:25:07:C3:96:93:75:F8:1D:05:C2:95:A7:1C:22:BD root@localhost (ssh-rsa)
:: [   PASS   ] :: Running 'ipa user-add root --first Fake --last Root --sshpubkey="ssh-rsa AAAAB3NzaC1yc2EAAAABIwAAAQEAx0Hg3CZIzizMIohZydE5+cSgIyByWmD0r/J5+k2P0AveG4i5lVFhcuMasK6VYBKSrFxSgpgkw5M82Ven2lyDpFoPbPJFE8KW6eLoRPCYPO+BBaI2j9t90HueoT2y1NBrKo0QTk5fCSSGN3kKuMUCgcqQw/9ea39dFAI96szAVfk+Y1eg1E84iOg1a/usFft0r+UuOd6bxzu/1lDHo522tIhiQCKAAyxOGij3w6Zw4mfFu/99l3LKm+ACAFpeAWkJqCjfku2WIkE1qo4+lU+8SIKpFkhJIjl9JnG/9ecuMWAhiZq9Ny4lypXogbVOPZThd2nAP3x+//t7+Vrq+VXjCQ== root@localhost"'
spawn ssh -o StrictHostKeyChecking=no root@localhost
Warning: Permanently added 'localhost' (RSA) to the list of known hosts.

root@localhost's password: 
Permission denied, please try again.

root@localhost's password: 
Permission denied, please try again.

root@localhost's password: 
Permission denied (publickey,gssapi-keyex,gssapi-with-mic,password).

:: [   PASS   ] :: BZ-886091 is not found : root SSH public key authentication is disallowed

Since the problem described in this bug report should be
resolved in a recent advisory, it has been closed with a
resolution of ERRATA.

For information on the advisory, and where to find the updated
files, follow the link below.

If the solution does not work for you, open a new bug report.

http://rhn.redhat.com/errata/RHSA-2013-0508.html