Use only programmer power
Looking at the manual I would say it's probably not a good idea.  

It may draw too much current for your programmer (you would have to verify this yourself) and also looking at the schematic there is a linear regulator that may not like having Vcc on it's output whilst nothing is on it's input.  

Unless you can confirm that neither of these point would cause possible problems, I would stick with (fully charged) batteries. Especially given the numerous warnings saying losing power during programming may permanently disable the 3pi.