First of all, while there were several opinions about CDG not being an attack. Non of them sounds logical to me. Personally, I am thinking that issue is already settled. It is doable.
I am estimating that for the party of current campaign, this assault will be just a good challenge and for players, that will be a good opportunity to start thinking about establishing counter-planer-attack methods for the current party. We are planning to play all the Adventure Path modules to the end as a farewell campaign for DnD 3.Xe. That means, in the next two modules, they must confront at least similar planar assaults and inter-planar travels. And scry/teleport,too. Sooner or later they must realize that their PCs have come to the level range that they must prepare for such assaults.
The majority of the players are experienced enough (or in other words, poisoned by various nasty adventures of various fantasy RPGs enough) to have watches even when sleeping in an assumed to be safe inn. And I will not let the Ninja automatically attack when some particular PCs are sleeping. I will roll randomly when the attack occurs. So, if the roll favor the PCs, that the Ninja cannot make that initial CDG at all.
As already wrote, there are two clerics who can cast Gentle Repose and Revivify. And there is another Sorcerer who can copy those spells via Limited Wish. And, the Ninja will likely to lose the majority of her Ki use per day during the search for the PCs. And all the PCs have some kind of temporal countermeasure against invisible/ethereal things. After making the initial attack, single Ninja have no chance for winning against entire party of PCs, even if one PC is non-operational and some others are not wearing armor.
So, I am estimating that no PCs will likely lose a level at all and all the PCs will start the adventure without trouble from the next morning. It will be one level loss of a character at worst and it is unlikely to happen. Maybe the sorcerer need to cast a Limited Wish for copying Gentle Repose but that is just a 300XP loss. 1-2 PC death is not that much of a trouble at this level.
PCs knows that the BBEG have some control and surveillance system in the dungeon. Actually, they have already destroyed many of the BBEG's "magical video camera" kind of sensors.
And they are sleeping in a part of the dungeon which are occupied by creatures hostile against the BBEG but have no guts to confront him by themselves. So it is not difficult for players to ascertain that the BBEG will know that PCs are using that part of the dungeon as their base camp. Actually, that will be the 3rd night the PCs use that camp. So I think they will not wonder why the BBEG found that PCs are sleeping in that part of the dungeon.
The vampire dominating some of the local creatures and forcing them to attack the PCs, then surprising the PCs when he starts stabbing them from ethereal sounds like SOOO much more fun to me. Then the PCs can decide for themselves if sleeping in such a vulnerable place is such a good idea.
Unfortunately, that plan don't work in this particular case. Vampire's domination refer to Dominate Person and not Dominate Monster. Thus it affects only on Humanoids. Those friendly creatures are Magical Beasts. I guess that is one of the reason why vampires are not enslaving all of those creatures already in the module.