AVR ISP-Programing LEDs SCK
Arduino's have a LED connected to pin 13 SCK (and have no problem)


Yes they do , but take a look at a typical schematic of Arduino UNO (as an example)



As you can see the SCK pin is connected to an OPAMP wired as a buffer which then drives the LED. The effect of that, is that the SCK pin only sees as a load the high input impedance of the OPAMP, so the pin can be easily driven by the programmer.


  However on MISO this never happens


The MISO pin is the slave output and in this case the slave is the AVR which apparently has a higher drive ability compared to the programmer and can successfully drive the output even with the LED attached.

If you want to use a LED then you should ether use a high impedance driver (like an OPAMP, a comparator, a mosfet etc), or you can use a jumper to detach the LED while programming.