SD cards seem to be very tolerant for delays in SPI transfers. I have delayed for many milliseconds mid-transfer with no problem.
Many people call analogRead() for several pins in an ISR while data is being written to the SD with no problem. Each call takes about 120 microseconds.
SdFat uses millis() to detect timeout errors so spending more than a millisecond in an ISR will cause millis() to drop counts. This should just extend the length for a timeout error.