I would put a pullup on the CS coming from the ATMega - then when the ATMega pins are inputs after a reset, power cycle, etc. for some undetermined time until your skeetch starts and makes the pin an output and drives it high, the CS line will be ensured to be high by the external pullup resistor and not corrupt the SD card.
"As for the card detect pins, there are no more pins available to connect them to"
Then no pullup is needed. Those are mechanical switches that are opened/closed with card insertion. If you are not going to detect hi/lo on them, you don't need pullups.