The implication that security could be preserved as mentioned previously in this thread is laughable. All OSs are patched against known exploits. Does this imply that there will be no more virus/worms/etc? Autodownloads means one server could cause all sorts of problems, perhaps so quietly that the user won't know, to all sorts of people.
It should be disabled on download and offered to be turned on, per server would be best IMO. It is the typical newbie coder attitude of "its fixed, what could possibly go wrong?" that should be avoided. I've dealt with it for years. "Sure, change these DB constraints on the production DB. It only changes this, what could possibly go wrong?" Then I watch as a server farm drops like a rock.
Having a system that downloads code means you need to control the place the code is distributed from. If you cannot do that, which tremulous clearly cannot due to its nature of independent servers, then you need to make the user decide to put their machine at risk. Your not enabling it on install is the warning that it is a security risk. Computer security 101.
cue the complaints that browsers do that. Yes, see the javascript/flash/ad nauseum methods of infecting/breaking/rooting computers. Then realize that the people making browsers, even OSS, have paid employees working on it to wake up at 2am to code a workaround and they have automated distribution channels, and computer professionals expect them to have serious security issues due to their nature.