The coordinator is the closed source piece of software that makes IOTA secure, no clone can exist until it is no longer needed. And still, even if coins were safe at the risk of network disruption, should a $5B project be purposefully leaving itself open to attack to avoid someone copying their code?

If you want to prevent your code being used by other people, then you make it closed source. Personally, I'm not at all confident that there are not more "copy protections" in the IOTA source code waiting to be discovered and exploited. The entire point of making a cryptocurrency open source is to show that there are no exploits or bad behavior, and IOTA has proven that this was not their reason for open sourcing it. Rather their reason seems to be to get contributions from the community and because no one would invest in a closed source cryptocurrency, especially not at the time of their "ICO"