Ems can still talk to one another and convince one another of things. How do we know they won't all be hijacked by meme-viruses, and transformed Agent Smith style?

This one is a little silly. Humans get hijacked by meme-viruses as well, all the time; it does cause problems, but mostly other humans manage to keep them line.

But as for the rest, yes, I agree with you that an upload scenario would have huge risks as well. Not to mention the fact that there might be a considerable pressure towards uploads merging together and ceasing to be individuals in any meaningful sense of the term. Humanity's future seems pretty hopeless to me.