"Note that while does not always refer to time. It is also used to balance two ideas that contrast with, but do not contradict, each other. In this sense, it is similar to whereas. Consider the following:

'While I like all types of fish, my girlfriend always chooses meat dishes when we go out to eat.'

'Some married couples argue all time, whereas others never do.'

'We would always choose somewhere in the mountains for a holiday, while our children always want the seaside.' "

http://www.bbc.co.uk/worldservice/learningenglish/grammar/learnit/learnitv69.shtml

I understand that, without the comma, it may cause some ambiguity in this particular case, creating two meanings, one of which does not relay the meaning of "pedig". However, not only would one of those meanings be correctly relaying the idea of "pedig", the use of "and" (which was accepted) would also present such problem.

Moreover, if the comma is present, it eliminates such an ambiguity, and I see no problem in its usage.

Az orvos megvizsgálja a beteget, míg mi kifestjük a falakat. Ebben a mondatban a két cselekmény biztosan azonos időben történik. The two acts take place in the same time in this sentence.

"Az orvos megvizsgálja a beteget, mi pedig kifestjük a falakat." A két cselekmény nem feltétlenül azonos időben történik. The two acts are not necessarily in the same time.