According to shieldlist the mSD shield uses pin 13 - 10 for SPI but this would basically mean that I would need to have two SPI busses running - one over ISCP and one over 13 - 10.
On the Arduino Uno (but not Mega) the SPI lines on the ICSP header and pins 10-13 are the same (i.e. physically connected to each other on the Arduino board). So you should be fine if the shield connects to pins 10 to 13.
Because on the Arduino Mega pins 10--13 are not the hardware SPI which are on pins 50--53 instead. The ICSP header gets the hardware SPI pins whichever board. General purpose shields using SPI use the ICSP header for this reason