Here's a thought, have the alchemist trap the room with flasks of Alchemists Fire (quantity GM's Discresion) hidden in the ceiling and they can be dropped all at once. When he drops the Darkness, the thugs duck into trap doors in the floor, and the Alchemist (Observing from above) releases the flasks. If your wanting to annoy more than maime, then consider spacing the flasks 1 per 10 feet increment.
*Queue Mad Alchemist Evil Laugh*
I had an Alchemist villain as well in one of my games.
She was a Tengu Alchemist, and had a sister who was an Inquisitor.
She was quite insane. She had fleet, and some magic items to increase movement, plus a headband of intellect that gave her acrobatics.
She would run and flip around the battlefield, cackling like a mad crow and toss explosive bombs on people and then skip away. :)
Drove the PCs absolutely insane. :)
I'd second the alchemist's fire, and add in a very simple method to drop it into combat--a chandelier made of individual oil lamps. Mount them in the middle of a wrought iron frame, put them in a stone room with nothing else flammable, and you're good to go.