Okay, I'm going to try not to contaminate this discussion too much, but I had to reply to this, because it's an excellent point.
When being alive does not merit respect, then why should he respect the existence of others?
Most people respect the existence of others, because they wish to have their own existence respected by others in turn. They believe that by doing so, they make it likely that others will respect their existence because they assume that others feel the same way and are willing to reciprocate.
If he didn't wish to have his own existence respected by others, then his actions make sense. He did what he had to do because of what he believed in (kill those people), and then we did what we had to do because of what we believed in (imprison him). That's all. Society and the unabomber just had a difference of opinion on morality that wasn't easily reconciled, and one of them had to yield. Since society was stronger, it was he who had to yield. So in the end, it doesn't matter if what we did was right (if there is such a thing as "right"), it was what our moral code dictated, because it was necessary to protect people, and we had the power to enforce it, so we did.
His biggest mistake, was simply acting alone. Had he recruited a large enough group of followers willing to challenge society for his ideals (and possibly blow up more buildings), we would have been forced to respect him whether we wanted to or not. He might have even managed to achieve whatever he set out to achieve, rather than just "send a message." One man has little power, but a group is very powerful.
Morality, in a given situation, is ultimately decided based on maintaining power, order, and politics, though we would all
like to believe that it's based on something else.