How to secure Drupal for closed user group?

Thank you for the clarification regarding VPN. If just HTTPS connections are allowed, does this mean that file attachments get encrypted for the transfer, too?

Yep pretty much everything in and out of Drupal is HTTP (or HTTPS i your case) - even uploads. There are some exceptions eg SMTP messages (it sounds like you won't be doing that though).

Is there a possibility to save the content (nodes) in encrypted form into the database? And to encrypt the directory where file attachments are stored?
The idea behind this is that if someone manages to break into the server, he/she could not use the data available.

This is where security paranoia departs the real world :)

If you are encrypting everything - what do you encrypt it with? Symmetric keys? Public Keys? A server key? A unique per user key?

If it's a server key - the key gets compromised when the server does. If it's a per user key - how does anyone read anybody elses content?

Assuming you do manage to create a secure user friendly PKI system that actually works - does your content travel all the way out of the database to the browser encrypted? Or does the web server (ie Apache/PHP/Drupal) need to decrypt it before reencrypting it as SSL. If it gets decrypted on the server, the someone with root can still get the content at that stage. If it stays encrypted all the way through - won't you have to build some decryption mechanism into the users browser?

And per user keys would still be the weak link in the chain - presumably you can't harden all their client machines to the same extent that the server is? Who knows what they'll end up installing or getting infected with.

However, this would only give additional security if the key to decrypt was supplied by the (regular) user (key not stored on the server).

Yep.

Realistically if someone gets root on your server - you're screwed. No amount of making life more difficult for your users is going to get around that. Your efforts should go into hardening the server so it doesn't get rooted.

Organisations that require that amount of paranoia wouldn't be connected to the internet at all (or supposed 'air gaps' at the very least), and would have tons of physical security too. I would think that if your NGO is like that, you wouldn't need (or even be allowed) to ask for security advice here :)

Encryption is hard, and unless you are using well proven built in stuff like SSL/TLS don't bother unless your really really know what your are doing.

You'd get better bang for your buck from traditional server hardening efforts. I think the following setup is beyond paranoid (and I wouldn't go anywhere near this far), but hey you might get some ideas:

Dedicated server with good physical security. Use a specially hardened OS like SELinux, Trusted Solaris, Trusted BSD (if it still exists) etc - and spend ages completely hardening all the kernel access stuff. All server software hardened and chrooted/jailed etc. All client machines are physically secure, hardened and on static IPs with smartcard based logins. Server authentication uses SSL client certs. Server firewall only accepts connections from the client IPs

But lets face it - if security was that important, you wouldn't be using a PHP based web app would you? :)

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Anton