Doug over at DMTF has written an excellent article about what do for OCS single sign on when internal domain and sip domain does not match. When split brain DNS is no option you can create two dns zones for the SRV records only. Here is an excerpt from his blog. View the full blog post here: http://blogs.technet.com/dougl/archive/2009/06/12/communicator-automatic-configuration-and-split-brain-dns.aspx

To implement this for Contoso, we would create a zone “_sipinternaltls._tcp.contoso.com” and zone “sip.contoso.com.” Notice that these are two zones – not two records in one “contoso.com” zone. A zone is a name resolution boundary in the hierarchical DNS namespace. By configuring the internal DNS server to be authoritative only for these two names, clients will continue resolving other names in the contoso.com domain as they always have.

Coincidentally, over on his blog, Geoff Clark has just suggested the same thing. He describes the problem and suggests the same solution but shows a method of creating the zone on a Windows DNS server via the DNS management console. Unfortunately, there is a limitation in the management console that is not present in the underlying Windows DNS implementation. This limitation required Geoff to create the zone as “_tcp.contoso.com” when what we would really like is a zone named “_sipinternaltls._tcp.contoso.com.”

This limitation in the user interface can be resolved by creating the zones and the records using the Dnscmd command line tool. For Contoso, here are the required commands:

dnscmd . /zoneadd _sipinternaltls._tcp.contoso.com. /dsprimary
dnscmd . /recordadd _sipinternaltls._tcp.contoso.com. @ SRV 0 0 5061 sip.contoso.com.
dnscmd . /zoneadd sip.contoso.com. /dsprimary
dnscmd . /recordadd sip.contoso.com. @ A 172.16.45.12

Of course, you’ll need to make the appropriate changes for your environment. If you are not running the command on your Windows DNS server, you will need to replace the first dot with your server name. You may also prefer a different zone type than “dsprimary.” If so, change the zoneadd commands appropriately. I doubt that your pool’s IP address is the same as my example but, if you have followed me this far, you already know what to change there.