Are there currently any alternatives, in terms of secure email providers? I never even knew it was a thing before the lavabit fiasco.
So yeah, my suggestion currently is to acknowledge the level of secrecy (or rather lack of) available with your email setup and use it accordingly.
This raises the barrier enough so that the NSA/FBI can't just request access to your mail. Instead now they would have to either physically access the mail server, or use extremely offensive techniques (backdoor your computer, take control of your mail server via a software vulnerability, etc).
Having said that, I'm in exactly the same position.
(Though I'm very seriously considering going back to running a mail server myself - probably on a RaspberryPi inside a locked cabinet at home…)
Even running your own mailserver (on a computer in your home, for example) won't save you from dragnet NSA surveillance or targeted attacks, but at least you'll know if the government sends you a National Security Letter or obtains a FISA court order for your email.
At which point you could disconnect your mail store from the server, stick it somewhere safe, and claim that you don't store mail, you just read it then delete it. They'd have to get a warrant to search your home, they'd probably decide it isn't worth it.
If you run your own MTA/IMAP server and lock down the OS and BIOS sufficiently -- including encrypting the hard drive -- you can be fairly confident that your at rest emails, including metadata, will not be accessed without your knowledge. But there's not much at all you can do to prevent mail sent to or from your machine from being intercepted. Configuring your MTA to only converse over TLS will help, but ultimately you have no good reason to trust the other mail server.
You can encrypt all your message bodies using either PGP or S/MAIL, but that requires the people you are conversing with the have key pairs, and doesn't protect metadata.
“If you knew what I know about e-mail, you might not use it either.”
Even more interesting is the fact that even Lavabit's founder seemed to have overlooked this fact, and instead of relocating his servers and all the user data to Iceland, Norway or New Zealand, he chose to shut it down for good.
Why?