Here's pretty much what I do:

ssh config:

    Host github.com gist.github.com
      Hostname %h
      User git
      RequestTTY no
      RemoteCommand none
      IdentitiesOnly yes
      ControlMaster no

    Match host github.com,gist.github.com exec "~/Developer/C++/getargv/getargv -0 -s 1 $PPID | env POSIXLY_CORRECT=1 xargs -0 getopt '46AaCfGgKkMNnqsTtVvXxYyB:b:c:D:E:e:F:I:i:J:L:l:m:O:o:p:Q:R:S:W:w:' | perl -pe 's|.*? -- ||' | fgrep -e username1"
      IdentityFile ~/.ssh/keys/github_rsa

    Match host github.com,gist.github.com exec "~/Developer/C++/getargv/getargv -0 -s 1 $PPID | env POSIXLY_CORRECT=1 xargs -0 getopt '46AaCfGgKkMNnqsTtVvXxYyB:b:c:D:E:e:F:I:i:J:L:l:m:O:o:p:Q:R:S:W:w:' | perl -pe 's|.*? -- ||' | fgrep -e username2"
      IdentityFile ~/.ssh/keys/github_rsa2

I set the common github configs in the top Host block, then each Match block looks at the arguments passed to ssh, parses them, and checks for the github username and if it matches, sets the correct key.

The ~/Developer/C++/getargv/getargv program is just an implementation of `cat /proc/$PPID/cmdline` for macOS, on linux you don't need a separate tool.

This works for cloning, pushing, pulling, etc.