There should be no auto-include neutral cards in Hearthstone. Period.
And what exactly are we talking about being auto-include? "Bad" Silence minions? They're tech options. Tech options are run to counter things so, yes, they're meant to be "auto-include in every deck" ... until they're no longer needed, anyway. Then they rotate out. Black Knight, Big Game Hunter, Harrison Jones / Acidic Swamp Ooze, etc. all fit this niche. Cards that are bad in a vacuum but good in specific instances. Maybe it's an agree to disagree case but I think these sorts of things are healthy for the game as it serves as a way to keep the meta in check.
As for the strength of Nerubian Egg, it's hard to say much about it yet. It's a really good card and the best way to deal with it isn't really ideal currently. Beyond that, it works really well with buffs which makes it really easy to trigger. Until we see how Shaman and Priest shape up with all their cards, I'm not really sure we can say that Egg is way too strong because of Zoo. To be fair, there's a non-zero chance that Egg just ends up being really good at creating weird niches for those classes (and, hell, possibly Paladin too) which comes back to your original point about Egg itself being too good but I'm not sure if that's really a problem then. Like, it serving as a big part of multiple decks is fine to me.
Honestly, you're just tunnel-visioning into Zoo like everyone else in this thread.
Hyperbole and venting aside, most of them just dislike it due to the popularity. At least, that's what I tell myself so I don't think everyone in the thread would like to bludgeon Zoo players to death.
Edit: I'm really curious as to how the Zoo style of play will be dealt with, though. With the game being so attacker advantaged, it's really hard to argue against Zoo's game plan. Use the best early game minions to put on pressure and control the board and dictate the pace of the game. The best way to deal with that is to ... out board control it or to survive until you wipe it all out. The problem is the former solution merely pits Zoo vs Zoo and the latter is too inconsistent (or simply too slow). Naxx is currently shaping up to try and fix that via a few class specific solutions but I'm not sold on it yet due to them not sounding consistent enough on paper.
Which again is why I find this unlock system so fucking bizarre. It just makes a mess of the meta for awhile on top of the whole "HEY THIS WORKS SO WELL oh wait not really" new card problem.