Mana is an issue, but that's not a problem with a disc rotation, but rather a problem with the much reduced mana regeneration in legion compared to wod. We can solve this by either doing the Vanilla thing of just stopping spellcasting altogether during slow times of the fight or using a mana-reduced rotation cutting out some of the atoned players, or perhaps radically altering our playstyle, forgoing damage and relying on The Penitent, Plea, PWS, Grace, Clarity of Will, and Shadow Covenant for healing.
Here's the math on Penance downtime -
Pen/Smi > Smite (no revelation, end of damage phase) > PWS > PtW > SM > PWR > PWS > Schism (start of damage phase) > Penance
In the worst case scenario revelation doesn't proc a single time during the damage phase. With 20% haste there's a 34.3% chance of this happening, with the damage phase being Penance > Smite > Smite > Smite (end of damage phase). A bit more haste allows another Smite cast and lowers the chance of no revelations to 24%.
In the worst case scenario there's a lot of Penance downtime, but 65.7% to 76% of the time Penance is the next to last (usually) or last spell cast during the damage phase. So in the usual sequence of Penance (revelationed) > Smite (end of damage phase) > PWS > PtW > SM > PWR > PWS > Schism > Penance there's only 2.2 seconds of off-cooldown between the two Penances at 20% haste.
There's a simple solution to reducing that downtime further - less atoned players (a shorter atonement phase). This can be accommodated in dungeons, but in raids it's probably preferable to maximize the number of atoned players at the expense of less penance casts.
One possible change to the rotation is just how amazing Schism is for *direct* damage in light of the recent nerf to Penance, and this would help with Schism downtime. Let's compare the direct throughput of Penance versus Schism:
At 20% haste with the artifact trait to raise Penance damage by 6%, end-of-damage phase Penance's throughput is 347.8 Spellpower/second. Schism's, amazingly, is 333 SP/second! So we could simply add Schism at the end of the damage phase, to not only provide good damage/healing in itself, but boost the strength of PtW/SWP ticks over the next 6 seconds. The damage phase would then be (worst case revelations):
Schism > Penance > Smite > Smite > Smite > Schism (end of damage phase).
The major advantage of this is rotation flexibility - if the existing atoned players continue to need healing we can extend the damage phase of healing to them further - otherwise we switch to the typical atonement phase.
The downside is that the above rotation doesn't quite work, since there's only 4.96 seconds of casting between Schisms while Schism's cd is 6 seconds. So we'd have to add another Smite, or perhaps a PWS. This extension of the damage phase increases the value of Contrition somewhat (especially with respect to the 1st PWSed player, if the PWSes were used on different players).