programming 3.3V PIC32 board with pic32prog and PICkit 2
The PicKit2 can program 3.3V devices just fine. Look at the PK2 user guide, section 3.4.2:

3.4.2  The application circuit is powered externally
The PICkit 2 may
be used with application circuits powered externally between +5.0V and
+2.5V.

You should look at the whole chapter 3, and compare its requirements / recommendations with the schematic of the board you need to program. But if it has an ICD3 header you probably should be fine.
You can measure, before connecting the PK2 to your board, that it indeed does output the proper voltage on Vdd when controlled by pic32prog (about 3.3V).
(Updated after reading Majenko's answer who did indeed look at the source code)