I've actually got 5 instances running from a single install point. I run each instance with ini=<server##>.ini and there we go, each server has it's own configuration now, from one installation...
it na work as far as u dont start using mods and addons.
Altho and regarding the few disk space required by server files I would not recommend to use same files for multiple instances. You need to make sure logging is disabled, that no files will be written by the different processes, etc. Not worth even trying it.
I honestly don't think it'd be a problem. I run all my TF2 and L4D servers like this. I realize KF requires very little disk space, but I'd still rather keep one instance of installation just to keep management simple.
I've been running like this since release now and not experiencing any trouble.