Is there anyway in 0009 to use my avrisp mkii to burn sketches sans bootloader?
I just did this with 0008, but outside the IDE. After you "upload" (even if you upload to a port with no Arduino on it) there's a .hex file in the applet subdirectory of the sketch directory (which works out to ~/Documents/Arduino/sketchname/applet/sketchname.hex on os X). Outside the IDE, just pop open a terminal window and use avrdude to burn the hex file.
I haven't played with 0009 yet, but if direct burning with the avrispmkII is a problem, I'd like to see a .hex file after a "verify" so we could skip the slightly messy process of trying to download to a device that isn't there.