I’ve been a happy user of Secretive for years, including for Git commit signature which it make it a separate key with interaction but not for pull / push. I find the trade off ideal for GitHub.com and have other keys with different setup for servers.
SSH keys in plaintext was one of the first thing that bagel [0] our developer endpoint secret detection focused on. Then we embedded bagel as a library in our developer endpoint protection [1].
[0] https://boostsecurityio.github.io/bagel/ [1] https://boostsecurityio.github.io/dazio/docs/install/