I generally agree with what you're saying but one thing I wish more people would realize is that the EB is divided into two sections: the Micropedia and the Macropedia. The Micropedia (actually Micropaedia) is what people generally think of when they think of encyclopedias: relatively short articles on a wide number of subjects. The Macropaedia had much longer articles that went into some depth on a much narrower number of topics. The articles on Number Theory and Relativity are a couple that stand out in my mind as being quite interesting to my younger self. The maps of select world cities were also a great source of interest to me. Wikipedia did not come close to this type of depth and organization until the last couple of years. In some areas they may still be behind: Macropaedia
I wouldn't say that religion poisons everything but rather that inflexible certitude poisons everything.
Now that's ironic . . .
Couldn't this too be easily done in an online social network-type setting? Some type of "karma points" system could be set up that would reward thoughtful review and criticism. Different weights could be placed on different opinions (for instance, a recognized expert in a field could be given a "karma boost") and some type of filtering could be instituted. Different teams of scientists who have replicated the experiment can publish their comments and findings in a way that links it to the original research. Citations of other papers would be linked in this way as well, of course. This seems to me to be the best direction to head in.
All great ideas are controversial, or have been at one time.