Thanks for the suggestion! I thought for them to be British colonies style, a symbol on the left and the national flag.
If you're going for British-colony-style then how about something like this?
The colour of the ensign would be different depending on the nation, but the top right should be the "coloniser" though probably the CIS doesn't want to look like a coloniser...
I also thought of this alternate design:
Instead of the CIS logo being a solid flag that must appear somewhere, the individual nationality comes first, and the CIS logo is displayed in the top-left of the flag (where the hammer and sickle would usually go).