Yes, Divine and the Skeleton shrines are the two shrines that present issues to the bot, and there's no short term solution for them aside from writing a plugin to logout if you come across them. Assuming they will be added to the core game, we'll eventually have to rework things to avoid the current issue as to why they pose a problem.
The core issue is that there is no way currently to implement the logic needed to handle that scenario with the design that the bot is currently using, in terms of tagging the shrine in a way that works for most people (and wouldn't result in the bot getting destroyed in the process).
We can add logic for the bot to ignore those shrines and mobs under its effects, but I've not actually come across them yet, still. If it seems like they are spawning more now, I can try to find some, but it's just one of those things that takes a lot of time to find, and if you don't actually find them, that time is kinda wasted.
If you find either of those shrines in Cruel or Normal and want to share the instance with me, I could take a look at working in something better, but right now PoE login seems down for me so I can't get on. You can PM me for Skype info though if you want to let me know when you come across one. I'l try to get a character into merciless soon if that's the only place you're botting.
This has been on the todo list for a while now, but priority wise, there's just been other things to do.