A Large value pull-up on MISO won't hurt but it is not needed. I bet you have another problem that is not really fixed.
I recently had a user make a similar claim but the real problem was chip select was floating due to bad wiring. A pull-up on a data line quieted noise on the nearby floating chip select and it went low long enough for the SD to initialize. The problem came back when lots of data was read from the SD. The 50 K internal SD CS pull-up resistor doesn't control chip select on most modules because level shifters over power it.
The SD card pads are bi-directional with tri-state drivers, and are in a high impedance state until enabled by the SD card, which may not be when the CS line is asserted as the card is not in SPI mode initially. Leaving any digital signal in a floating, unknown, state is not a good idea.
SPI should not have pull-ups or pull-downs on MISO, MOSI, or SCK. There is not a default state since there are four SPI modes and the SD is not the only device on the bus. Why would you pull MISO to 3.3 V on a 5 V system?
Atmel doesn't suggest pull-anything resistors in the processor datasheet. In fact Atmel suggests not using pull-ups/downs in some configurations.
The fact that pull-ups are not required is often stated as an advantage of SPI.
Typically lower power requirements than I²C or SMBus due to less circuitry (including pull up resistors)
It probably works without the pull-ups most of the time, but I found a case where it doesn't, and that's why pull-ups are required, so it will work all of the time.
I don't believe you found a case but you may be the first. I wrote SdFat, which is also the base for the Arduino SD.h library. You are not the first to make this type of claim. This type of "fix" means there is another problem that is the real cause and it will likely bite again.
I was involved with Limor Fried on design of Adafruit SD modules and I believe her design is sound and no pull-ups are needed.
Read the SD association's SD "Physical Layer Simplified Specification". The only mention of pull-up for SPI is the 50 K card detect/CS pullup that must be driven low during initialization to select SPI mode. This is not the DO pin in SPI mode.
There is mention of pullups for the new UHS-II pins 10-17 but these are not relevant here.