Freenode has absolutely no innate responsibility to extend trust to a third party such as Mibbit. I see no reason to judge them poorly for failing to do so, or how this reflects on Mibbit's integrity.
They don't have any responsibility to provide it, they can do what they like to their users. But I think their users liked it - which is why thousands of people used mibbit to connect to freenode.
Freenode clearly has a closed management culture, which is why they want complete control of everything. I don't think that makes for a great community.
Provide a friendly interaction environment for project coordination and for the support of community projects.
Freenode, as a communication platform (and particularly as a self-described "friendly" environment) have a duty, to common sense and intelligence, to make reasonable efforts to encourage communication rather than stifle it.
Being willfully wooden-headed about this whole thing is not just wrong because of the unnecessary harm it causes, it's also self-contradictory.
What about Facebook? Google Talk?
As a member of several "community projects", I don't feel particularly slighted (and am, in fact, relieved due to decreased abuse) by the disconnection of Mibbit.