As for the loss of stats and the corruption points: There is no doubt that should happen. The Mass Possession peril specifically references the Possession trait, which in turn makes it clear that if the daemon is cast out by exorcism OR ANY OTHER MEANS, they get the 2d10 permanent strength and toughness damage.
As for keeping the stat increases (and/or wounds), well, it could go both ways. While I do believe some if it indeed comes from the psychic energy infusing the flesh, it also states it does feature physical warping of features and flesh. It's your own judgement call, really, but I'd probably provide a choice: keep it, and the daemon-warped flesh that grants it, or get it reversed and stop looking like you're still possessed by a warp entity.
From a purely "rules lawyer" perspective however, they would get to keep it. The rules state the victim increases it's strength and toughness, and gains more wounds. Nowhere is it mentioned that it goes away if the possession ends, nor even implied. So going by rules as written alone, they would indeed get to keep both the wounds, the stat increases (but also suffer the 2d10 decreases) and any mutations you decided to give them. However, by that same token, nowhere does it say the horrible, daemon warped visage of the possessed goes away either.
@Gurkhal. I'm not really sure I can agree with the sentiment "If they get something free, take something away" mentality. If players provide a clear, logical reason for why they ought to get something as a consequence of something else, they ought to get it. Likewise, if there's a clear, logical reason they ought to lose something, they ought to lose it. In this case, they have the logically sound argument "We got stronger because a daemon warped our flesh to it's liking", which holds water. They also had the not so sound argument "it was temporary, therefore we should only get the bonuses, not the penalties", which doesn't hold water and thus they ought to get the penalties.
The fact that they presented their argument is certainly not grounds to ignore it.