A single “entire” instance being ruined is a much smaller problem than a whole platform.
As for the duplicate community problem, I would love to see either a multi-reddit-like feature or the ability to merge/co-mingle “duplicate” communities across instances.
The solution to tyrannical mods or admins is simple: “take your ball and go home” by starting your own instance, or your own community on a separate instance. That said, instances and communities grow by growing trust between users and mods/admins by a track record of acting in a rational and trustworthy way.
Privacy is definitely a problem for Lemmy. You should assume everything you post or comment is public and in the open, and impossible to fully delete, because it is. Post accordingly. You could theoretically be identified by the sum total of all personally identifying information you freely post over a long enough time or by your writing style if a government considered you a real threat.
That said, many instances do not even require an email address. I don’t know whether instances store data like IP addresses, but you could check the lemmy source code to find out.
Edit: But also, who’s to say their server source code is unaltered? Federation lives and dies by trust and mutual cooperation, and that cannot be guaranteed.