So I dunno if this has been suggested by anyone before, but I wanna put forward High Priest Hester for my guess at who is holding Ivala. My reasons are as follows: During one of the chapter interlude scenes a conversation between Ivala and someone else (can't remember if it was Mithyn or Tanaruk) I got the impression that whoever was holding her was female. It's been mentioned that whoever is manipulating the tower to create the chosen is using tower magic but only on a real world level (I'm not saying this well. Only to effect shallowly at the real world?) and I feel this is because whoever it is doesn't care about the tower or great magic, they only care about the real world (and faith in Ivala). After Estevan's worldwide announcement about fucking all the goddesses, Hester in particular was mentioned as looking furious. And shortly afterwards the crystal appears in Ardford (where Hester was at the time of the announcement) and the number of Chosen significantly increases. Hester keeps going on about retiring once she has got the church and it's future in order (and using Ivala's magic to accomplish this?). Plus it's fairly obvious someone high up in the church is behind the chosen anyway and quite frankly, none of the other high priestesses seem intelligent enough.
So that leaves overall motive. My guess would be that, like King Alonon, Hester has taken a peek through the tower at the fundimental nature of the world. Perhaps even she did it with him. And my guess is that, like Alonon, the experience left her somewhat broken. Most likely for Hester it would be the realization that Ivala wasn't all powerful, and that goddesses as a whole were petty little powerholders. And so she has chosen to take that power and try to make it what she belives it should of been.
On a side note, if what was stated earlier about Xerces holding Zelica is correct, and with Tanaruk hunting Mithyn, then we seem to be heading for a divine shard nuclear stand-off. We have Tertia, Xerces has Zelica, Hester* has Ivala, Tanaruk will get Mithyn. Only the Mother will be free to upset the balance or wait for a 5th major player (Lillith or Mestan?) to enter the stage.