You kind of put the cart before the horse... Threads are the coping mechanism, that has to cope with signals, not the other way around. Threads exist in the way they are because of the original bad design (which included signals).
Potentially, there could be other ways of dealing with communication, some of them already exist in popular operating systems, s.a. sockets. It's actually funny that you mention one in your problem statement. Erlang-style ports are another possible solution.
Replace “thread” with “process”, then. The basic fact doesn't really change; if you want a clean shutdown on Ctrl-C, you'll need to allow an EINTR-like return from a blocking syscall.
Potentially, there could be other ways of dealing with communication, some of them already exist in popular operating systems, s.a. sockets. It's actually funny that you mention one in your problem statement. Erlang-style ports are another possible solution.