The fact that Stealth Bombers can land on Carriers is covered by the:
<Special>SPECIALUNIT_FIGHTER</Special>
tag in CIV5Units.xml file.
You can remove this from the Stealth Bomber and they won't be able to land on Carriers, but as a consequence they may not be loadable into cities anymore (per CIV5SpecialUnits.xml)
Work with CIV5SpecialUnits.xml for the solution. I'd do it myself, but I'm not much of a programmer...
As a possible solution, I'd recommend creating another called SPECIALUNIT_BOMBER in CIV5SpecialUnits.xml:
<Row>
<Type>SPECIALUNIT_BOMBER</Type>
<Description>TXT_KEY_SPECIALUNIT_BOMBER</Description>
<Valid>true</Valid>
<CityLoad>true</CityLoad>
</Row>
and change <Special>SPECIALUNIT_FIGHTER</Special> to <Special>SPECIALUNIT_BOMBER</Special> for the Stealth Bomber in CIV5Units.xml. Thereby allowing the SB to be stacked in the cities, but not loadable on the Carrier...