"I looked at locking the content through htaccess to prevent direct access or hotlinking but it seems that would block many legit members trying to view the content on the site (something about firewalls). Any thoughts?"
No, I don't see why this would be the case. Maybe you could explain the "something about firewalls" part in more detail.
Anyhow, consider the situation where you have two Wordpress installations. They install to separate directories. The .htaccess file under one of the WP installation directories (your secure section) can prevent access to everything stored underneath it.
I've also heard of some different WP plugins that manage secure content, but haven't used them, so will leave it to others to recommend. It seems there are some nice ones out there, though. I was considering MagicMembers myself, since it integrates with CCBill.
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