I've accidently put a shutdown.desktop script in my
home/pi/.config/autostart directory. Because of this I am unable to start the pi again, is there a way to delete this file on my windows desktop? I use Rasbian Jessie.
Windows only knows about Window's partitions. Try putting the SD card in your machine and see if you can find the file.
If you can't the simplest thing to do is probably to boot your PC using a live Linux CD. That will let you access all partitions on the SD card.