Re: PicKit 2 with PIC16F886
Without the pull-up and with the switch open, the input pin will just be left floating. So this won’t work.
You could put jumpers on your board and disconnect the pull-ups when you want to program.
Or remove the pull-ups for the board and put them on a special plug you make and plug that into the programming header when not in use for programming.
Of course this won’t help you debugging if you need to debug the operation of the switches.