I'm pretty sure SSH wouldn't mind the config being a symlink to a file in your safely-held-elsewhere repository. Maybe I'm wrong. (m)DNS is what I'd really go for if I'm really just looking for easy access to names.

I wouldn't worry, but I also have the habit of adding things to the index explicitly. If I did worry: gitignore.

In fact, the symlink thing is exactly how we distribute the common ssh config as an included file within the team. The config is part of the infrastructure repo, and everyone gets a current version whenever they pull afresh.

I'm also not sure why version control on ssh config should be a problem, unless previous poster confuses version control and "send everything to the cloud".