If you edit the dat file by hand you can make this work. It's a little complicated if you copy/paste the base cleric panel stuff from srd_class_cleric.dat, because you'll have to rename a lot of the things to prevent duplicates... but open that file and find this code:
Code:
<layout
id="cleric">
<portalref portal="cClrDomSpl" taborder="60"/>
<portalref portal="cClrSpells" taborder="70"/>
<portalref portal="cClrDom1" taborder="40"/>
<portalref portal="cClrDom2" taborder="50"/>
Notice the 4 "portalref" statements below that? The last two of those are for the two Domains... if the 2nd one were removed, and any references to that second portal, it will only show 1 domain on the class panel.
Hope this makes sense!