We really need more info on the Plan
I agree with the dire consequences approach. If you simply have the badguys use their new found power to cast a non magical "transmute players to blood stain" on them, two things will happen.
1) Your players will be unhappy.
2) You will be unsatisfied.
For the short term, adapt the following for your next game session.
<b>"As you approach the portal, it shimmers, and a humanoid form staggers out. The creature is black and dirty, and making unfamiliar noises. Smoke rises off of its hunched back. As you get closer, you realize that this is no otherworldly creature. This is a young human male!
The young man is covered in blood, and stinks of his own excrement. Small maggot like creatures are crawling in and out of smouldering open sores on his legs, arms, and chest. Occasionally one hits the ground and staggers around. He falls to his knees and reaches out to you beeseechingly, and not so small bits of charred bleeding flesh fall off of his arms, ploping wetly on the dew covered grass. He tries to speak, but instead vomits up some bile, coughing and sputtering. He opens his eyes, his bloodshot eye and gaping empty socket bore into your souls as he finally manages to speak.
"Why?" He asks. "You could have saved us. You could have saved my infant son and my wife, my Wanda. Instead I was forced to watch as my wife was beaten to death with a flaming torch. I was forced to watch as my child had firely coals stuffed down his throat and torn apart by dogs. You could have saved us, but instead, you let them win! You cannot stop them now, but if you have any mercy or pity in you, please, save the others!".
His final damning words echo in your ears as he finally falls forward, dead."</b>
When the players get into the part of the dungeon (or whatever), have them fight some of the villians servants rather then the villians. The bad guys them selves are long gone, and have taken their treasures with them.
Then, decide on some pretty stiff consequences for the world, and apply them to your PRIMARY campaign world, and have them meet bards every now and then who tell the tale of the cowardly heroes who turned their backs on the innocent and snatched defeat from the jaws of victory.
END COMMUNICATION