In terms of conflicts of interest, the league should be looking out not only for actual conflicts (i.e., partiality) but also the appearance of impropriety. Things like this just shouldn't happen, regardless of whether the refs themselves lack bias.
I don't think the refereeing was nearly as bad as people are suggesting, but things like this story just give the conspiracy theorists something to hang their hat on. If a ref knows, subconsciously, that his son really wants to see the Bulls win, does that potentially impact his call? I would say that, again subconsciously, there's the chance that it does.