Regarding the suggestions in the OP:

1) Heck no for the reasons mentioned in the SCH thread. Changing Holy to be targeted akin to Gravity is 100% a nerf and substantial DPS loss even if you don't realise it. Holy has some unique advantages in it's current form that IMHO outweigh the 'disadvantage' of needing to close.

2) Thundercloud procs are something I've suggested and would absolutely get behind. 3x Holy after 3 glares I'm not so keen on, it's not got the unpredictability of procs so you're effectively making a 1112 rotation which is something, but a very meeeeh something IMO, I'd rather see something a bit more interesting that breaks up the monotony a bit... Like Thundercloud procs . (Also side note, assuming the cast time stayed as is, weaving on the Holy part of the rotation would be an issue).

3) I'd never say no to more Lilies, but I think it could be executed in a more satisfying stylish way. I'd suggest the following:

Holy has a 10% chance on hit to cause Dia on a target to detonate for it's remaining potency removing the dot in the process. This detonation will trigger any other Dia in a 5y radius to explode as well. Grants 1 additional Blood lily for every 3 targets hit by this detonation.

IMHO this would be neat but really quite deceptive. In a fairly typical 8 mob double trash pack pull you'd proc the detonation almost immediately and get a pair of Blood Lilies to boot likely landing you with a meaty upfront lump of potency right off the bat as you explode the full duration Dias and likely follow up with a Misery in the following GCD. The reality is that the only DPS gain is the extra Blood Lilies though, as assuming you're dotting mobs on the pull, it's generally the norm for dots to run their duration before the pack dies. If you genuinely wanted more damage, you could increase the power of this by having the detonation deal the full dot damage rather than just the remaining potency, but that may be a little strong on pulls that cover a longer distance.