Woohoo digging an old thread .

Now you can launch PicKit 2 within MCS. Just download PK2CMD command line interface at the following link
http://ww1.microchip.com/downloads/e...K2CMDv1-00.zip

unzip everything in your Pickit 2 folder, add a programmer in MCS (View >> compile and program option >> programmer tab), and use the following parameters...
Code:
/PPIC$target-device$ /f$hex-filename$ /M
Enjoy, and remember that there's an README file in the package too

Enjoy!