it's a good question, and one that's hard to answer in the end. Commentators in-game call out refs for "make up" calls, for players who get star treatment, home team calls, and I think it's safe to say even supposedly unbiased national commentators dispute a pretty high number of foul calls and non-calls.
as far as the league instructing officials on how to call a particular game, I think it probably does happen and that was the most troublesome aspect of Donaghy's accusations for me. Based on that alone i'd rate the trustworthiness of the nba as a 3.