Beginning with xl2007 there were some context-sensitive options added to the Conditional Formatting(CF) dialogs when applying formatting to PivotTables.
If you're not already familiar with the 3 types of "scoping" you can apply to a rule for a PivotTable, see this link which appears in Excel 2010's Help. (not sure if it's in xl2007's Help)
Add, change, find, or clear conditional formats - Excel - Office.com
Your question relates to this part of the description:
"If you change the layout of the PivotTable report, by filtering, hiding levels, collapsing and expanding levels, or moving a field, the conditional format is maintained, as long as the fields in the underlying data are not removed."
In my experience, this is not always true (or I might be misinterpreting the description).
PivotTable CF that is applied with "Scoping by value field" or "Scoping by corresponding field" seems to exhibit this behavior:
filtering: CF Maintained
hiding levels: I'm not postive what that means. CF is not Maintained when a field is deselected then reselected in the Field List.
collapsing and expanding levels: CF Maintained
moving a field: CF Maintained if changing the Position of a field within the same PivotTable area; Not Maintained if moved to another area.
Based on that (and I'd appreciate a correction if I have any of that wrong), I believe you'll need to use a VBA approach to achieve your desired result.
Here are links to two examples that take very different approaches.
This code by Doug Glancy stores the CF settings in a header cell, then reapplies the CF to the data range after a change.
http://yoursumbuddy.com/re-apply-excel-pivot-table-conditional-formatting/
The code by Jon Peltier uses VBA to test a condition and apply formatting instead of using Excel's CF Function.
Pivot Table Conditional Formatting with VBA | Peltier Tech Blog | Excel Charts
I'd be glad to help you adapt either of those examples, or develop alternative code if those don't suit your needs.
Looks like a big gap that could use a good general-purpose-code workaround.