Oh wow. Alright, I'll admit that was not the method I would've even imagined using to give the tree more punch in it's lunch but that's a creative way of doing it. Tossing around Maximized and Empowered Spellbook version of those debuffs would get expensive to do long term, but it's really nice to have as an option for tougher encounters, especially since they no longer share a CD with the SLA. Also makes it clear that you should be taking Max/Emp/Intense. I would go so far as to argue that it might even need to be watched for being overtuned on the proc. I think because of the SP cost for non SLA in addition to the CD for the SLA that there will be enough downtime to not tip into that range, but at the same time 2d6 every caster level (not sure what the MCL for the effect is, 25?) on a no save Meta-able damage effect is pretty potent.
Only thing I would note is maybe add a class feat, a note in the Core points in the enhancement tree, something in the description of the SLA's, or attached to Pray for Mercy that notes that the spells Bane/Prayer/Bestow Curse/etc can accept damaging Metamagics since that is most definitely a quirky addition that you would never guess on your own.
Seems like a simple change but I can see it having a great impact on making this tree much more viable. When I say simple i mean simple on the surface. I'm sure the coding for that is a royal nightmare.