@mahtan
Its both to an extent. We already know the queen is in on it from earlier chapters, and I don't doubt she has her hands in the church as well. The church likely also has other agendas for Eli, but still likely take orders from the queen about how to use her. She likely also freed the dad too somehow.
The real question is, do assassins not exist? It should not be hard to kill a few prisoner durring an escort if an earthquake can free him enough with out harming him to allow his escape, while pushing the carriage into a river. Like seriously, how did that get fuck up. The carriage was found in a river, yet the story blames an earthquake? Also, he is a prisoner, how can he escape a locked prisoner transport? They should not be taking him to a small jail, he is headed to maximum security for a life sentencing, so his transport would not be lightly guarded or just an open wagon (like in skyrim's opening) either. If anything, he should be dead in his transport from drowning in the river. This is assuming he was not just let go (which honestly is likely the case). Carriages don't just get into a river, with no personnel found around, week later (btw how do they know it was there for a week?). Sounds like a cover-up to me.