Does anyone really care about the WCC? In 2008, McLaren didn't seem too gutted in losing the WCC but you just have to see Ferrari's reaction when they lost the WDC.
Ferrari didn't seem to sad that they lost the WCC this year either.
Actually, having a #1 and #2 increases BOTH WDC and WCC chances. If you have a #1 and #2 driver and you swap them around when they are running 1 and 2 to maximise the #1 drivers points, like RBR had many chances to do this season. You still end up with the same WCC points but you build a buffer in the WDC race.
When you have two team mates taking points away from each other, any DNFS are costly as a driver is expected to have a couple of DNFs in the season. With the #1 and #2 driver situation you build a buffer to protect against such DNFs.