The publishing of the Muhammad cartoons in Denmark was the finest example of freedom of speech, and the very idea they should have been censored or suppressed is absolutely disgusting. The reality is no one would have come to the defense of Christians rioting around the world and killing people over Piss Christ.
Publishing controversial material and the freedom to do so is enshrined in the principles of democratic societies. Being willing to publish something that might make people angry, if there is a need for the material to be made public, is part of what journalists must do. But just because something can be published doesn't mean it should be. Doing something just to make a point, knowing it may unleash unrest is not advisable.
The question is this:
'Muhammad cartoons controversy: Did publishing the cartoons uphold free speech?'
No, publishing the cartoons was an /expression/ of free speech, it was not an /act of upholding/ free speech. There are only a few things that literally uphold free speech. Those things are laws, judgements, verdicts, etc.
An expression of free speech is not an act to uphold free speech. They are separate things. To defend the legal right of the publishers to publish the cartoon would be an act of upholding free speech. To rule that the cartoons were an expression of free speech would be an act to uphold free speech. The cartoons themselves were simply an expression of free speech.
Of course, it can be argued that because an act of free speech is an expression of free speech, and that because some rights needs to be flexed from time-to-time to ensure they are not eroded, the publishing of the cartoons was therefore an act to help maintain the right to free speech. This is not, however, the same thing as 'upholding a right'.
Flexing one's rights helps to maintain those rights, but ultimately, those rights can only be upheld by other processes.
(To make my own position clear: I totally agree that cartoonists should be able to publish anything they want about Mohammad, or any other figure. I am a free-speech absolutist... But that is not what the question asks).