Long story short, the party rescues a Changeling child and decides the best way to protect her in the long run is to help her form her own coven.
Now we are level 11 and she is a grown up 9th level witch with another witch and shaman as mentors, and is searching for an Iron Collar of the Unbound Coven to eliminate the need for an actual hag.
Will she be too powerful an ally at this point having access to these coven spells?
speak with dead,
It's assumed that she is not directly adventuring with the party, but if she were asked to help, there is no reason in the plot yet that she and the other members of the coven wouldn't help.
Should we roll with the coven rules as is or say that there is only a defective Iron Collar of the Unbound Coven with more restricted access to spells?
Even if you befriend a coven of NPC witches, it's not any more powerful than a PC witch doing the same thing and forming her own coven. Witches who belong to covens usually don't hang out with each other all the time, they typically do their own thing alone by themselves, and then meet up with the other coven members a couple times a year for rituals and blood moons, etc., and maybe some birthday parties :)
There are some covens that hang out with each other on a daily basis but I'd say that's kinda rare. So even if you do have an NPC witch hanging out with you for a particular side quest or short journey, she'd be no more powerful than a Cohort. She probably wouldn't be dragging the other coven members with her.
Short answer is no.
Regardless of the party having helped the Changeling, she is only one third of the Coven... the Coven, in its entirety, owes the party nothing. By the sounds of it, the other two members of the Coven are both more powerful than the Changeling... she probably has the smallest say in what the Coven does, so the party asking the Changeling to ask the Coven for a favor is unlikely, at best... be careful asking favors of witches.
I don't know why anyone would volunteer to have anything to do with a Coven. It's best they don't know you even exist, so you can never be a pawn in one of their stupid schemes. I would literally rather make deals with devils than any Coven.
I don’t see any reason to limit them… keep in mind, in order for a coven to use any of their spell-like abilities all 3 members must spend a full round action together to cast the spell like ability through ONE member… this means that until the third witch completes their full-round action the spell is in the process of being cast and can be disrupted. A single enemy attacking any witch who has completed their action will force a concentration check and if that witch fails the coven casting fails. If the coven has more than 3 members then the extra members could step in to help complete it still… but all that is assuming you even have 3 members of the coven with you…
Now, you said this NPC witch has been mentored by a higher level witch and shaman, whom I presume are 2 members of the actual party… if these are indeed players then I can see where the concern might come from, however, in any given round of combat an ordinary witch or shaman spell or hex is far more valuable than a coven spell. Coven spells are most useful out of combat.