It's not the 44.1 that's the problem, but the 88.2 and 176.4 rates which are lumped together with it. Every receiver out there with a digital input is able to handle both 44.1 and 48 kHz sampling rates.
I don't know why Sony choose to not make a "pure" option, and separate upsampling from the base rate. 44.1 kHz is required for DTS CDs to function correctly. It is possible to make the PS3 output 44.1 instead of upsampling, by going into the audio settings and removing the check boxes on the 88.2 and 176.4 modes. That's probably the best thing to do for anyone owning a non-SACD compatible PS3. But if you do play SACDs in the system you'll want to leave those higher rates enabled.
HDMI connections are able to specify which rates are supported during the handshake, so no compatibility issues should happen there. But for people using the optical connection, the PS3 can only go by what the user tells it. That's why it defaults to the 48, because that will always work.
