Ok, bit of Easter holiday coding today. Version 1.1.0 should allow connections to remote and already running kernels (well it does for me), and will only issue kernel shutdown messages if it started the kernel itself. To connect to a remote kernel, you can either manually fill in a cluster of port numbers etc, or simply paste the json from the connection file or (if you have an existing front end to the kernel) do:
from ipykernel.connect import get_connection_info
If starting kernels on another machine, remember to tell them to bind to an IP address that isn't localhost e.g. ipython kernel --ip=u.x.y.z and make sure the firewall will let the ports through.