I'm not sure I see the problem you're identifying. Although you're right about the collective ownership details of the project, surely the CICLA is only really concerning itself with the contribution itself?

That ought to be pretty much the sole property of whoever the contributor is. So even if Joe Hacker modified the (C) Canonical & mjg59 codebase, the agreement is only governing the patch (or whatever) to the extent that Joe Hacker holds rights to it. Yes, the patch is basically useless without the extra set of rights to the collective work, but I don't see how modifying that work means the patch itself is automatically (C) Canonical & mjg59 also.