He threatened to kill himself. And then he threatened to kill himself again because his "career was over".
While successful criminal charges may be life-changing, they are not automatically an end to your career, especially not a unique and special one as Mr. Murdock had. His career was one which he created for himself, which he was the main driving force of, and which was based on his accomplishments and reputation in the Linux and Open Source communities where it was basically unassailable, as should be obvious from a lot of the replies about his death.
There's a drastic leap of logic here needed to believe any of this to be true.
You think assaulting an officer is a trivial crime?
Well, instead of just emotionally asserting "facts", as you seem to want to do, let's take a look and see how serious it is. A quick google search reveals that:
Battery on a peace / police officer is typically a misdemeanor in California law. The potential penalties are up to one (1) year in county jail, and/or a fine of up to two thousand dollars ($2,000).4
But if the battery causes an injury requiring medical treatment, then this crime becomes a wobbler (that is, a crime that may be charged as a misdemeanor or a California felony).
If it is charged as a felony, battery on a peace officer carries a potential sentence of sixteen (16) months, two (2) or three (3) years in county jail, and/or a fine of up to ten thousand dollars ($10,000).5
Seeing as no police required medical treatment, and that the description of his arrest(s) and treatment don't seem to be out of the ordinary, he wasn't likely to be charged with a felony and wasn't likely to see jailtime. Considering he was in good standing with the community and had no prior arrests (?), he was probably going to receive IF FOUND GUILTY some combination of probation, fines, community service, or mental health treatment. Do you consider that to be "serious"? Or worth taking your life over?
The entire argument against this being anything other than a tragic suicide rests on making up "facts" and emotionally appealing to the state being able to do anything it wants, with the proof being the same thing as the question in the first place: that they just murdered Ian Murdock and are conspiring with his family members to cover it up.
I'm going to go with option (b) here, which is that his family desires privacy because he tragically took his own life in a way that never needed to happen and they don't want to drag his name through the mud. His family has more reasons than anybody to pursue the truth here.