The issue is not at all with his opinion. It is that he expressed it in a horrendously, gratuitously crass and offensive way. Here is a transliteration into humane language of what he said:
"My heart goes out to Steve Jobs' family in their time of grief. And my heart also goes to the millions of people who looked up to him as an icon and inspiration. But we need to not get so carried away honoring the dead that we forget the damage that Jobs' work had on the Free Software movement.
His pioneered the software walled garden, which destroys freedom and choice. And he targeted it at people who would not understand what they were sacrificing by giving up their freedoms.
We can only hope that his successors make Apple a more free company, or failing that, are not as effective at spreading it as he was."
Wasn't that better? And it communicated substantively the same thing, but without all the name calling and the seeming glee over the death of another human.
Disclaimer: I typed this on my Macbook Air.
Edit: One more thing to add. Saying "I'm not glad he's dead, but I'm glad he's gone" is tripe. Being gone is a euphemism for being dead. The reason we mourn when a loved one dies is precisely because that means they are gone.
Maybe RMS sees a subtle distinction between death and gone-ness in his head. But I promise you that people in grief see absolutely no distinction between the death and the loss of the person they mourn.