Ctrl-C in Emacs is not "terminate program", it is "start of user command", in most modes. Similarly, even in vi/vim, Ctrl-C does something completely different. So this has nothing to do with the terminal whatsoever.
It made sense that interrupt in Emacs could get into a controlled state of receiving the next command. It's a little bit like the SAK (secure attention key) concept, as seen with Windows use of ctrl-alt-del.
Edit: Ironically, as a long-term emacs user, I don't really remember any commands that start with ctrl-c! For me, the most common sequences start with ctrl-X or meta-X. Or the prefix search commands ctrl-S and ctrl-R.
Now, C-c in particular is the key stroke which non-core modes are recommended to use for their key binds (for example, sgml-mode uses C-c as a prefix for all of its commands, e.g. C-c C-f for sgml-skip-tag-forward, C-c C-b for sgml-skip-tag-backward, etc). Running `killall -SIGINT emacs` will not be interpreted as a C-c key being hit in emacs, it will just cause emacs to quit.
The same thing is true for other terminal based programs, like vi. Pressing Ctrl+C in vi does not generate an interrupt signal, it just passes this key combo to vi to do with as it pleases.