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You're right, but you're wrong.
It turns out each "member" of the family account does get their "own" cloud with which to sync, but there's nothing stopping you from all syncing to the same cloud.
Here's how I solved it.
I connected my wife's phone to MY cloud by adding my Mobile Me email account on her phone. Then I went into Settings and turned OFF "Mail", but left "Calendars", "Contacts", "Bookmarks" and "Find my iPhone" turned on.
Now, she's associated with my cloud for everything but email messages.
Her own Mobile Me e-mail is still set up as an email (only) account (and my account doesn't even show up when you go to Mail on the phone).
So, her syncing of everything (but mail) is done with "my" cloud, and her email is her own.