At the point where you're encrypting secrets in resident memory in a normal server program, you have gone fully into saffron-grade security. If you're worried about leaking secrets in your environment, overwrite the environment variable data and be done with it. In reality, if this is a real concern, unsetenv(3) is probably enough to avoid the actual attack vector --- a vulnerability where you leak environment variables qua environment variables (because you shell out or something).
Whatever vulnerability you're positing that leaks a secret out of arbitrary resident memory also leaks whatever secret you'd use to encrypt, and now you're not building a security system, you're building a DRM scheme. Don't let me yuck your yum on that, but: not a good ROI for security.
I do quibble with the statement that
> unsetenv(3) is probably enough to avoid the actual attack vector
It's not, because it doesn't modify the environment block of the process. Even if you use unsetenv, you're one path-traversal vuln away from folks being able to read all your startup-time secrets out of /proc/self/environ. Similar is true for exploits that can read process memory in small chunks: it takes time and risks detection to e.g. crawl around the stack/heap of who-knows-what-language to find interesting variables, but it's a lot easier to grab whatever's at the top of the stack by address (the env blob, which I think is also unmodified by most unsetenv(3) implementations). Path traversals and small-arbitrary-read exploits aren't exactly uncommon, and environment variables are the wp-admin/admin.php of exploit targets.
That's a quibble; you're broadly right, and that risk's not nearly severe enough to torture your code or bring in caching + encrypting runtime secret stores or whatnot.
I just wish env had been implemented without a /proc view and with reads requiring a cheap syscall rather than memory-residence, you know? Yeah, it's pointless to speculate about, but still seems like an obviously-preferable-in-retrospect road not taken.
"saffron-grade security" is pretty good, too.