My suggestion is to let the players play what they want to, and you DM what you want to, and reember you have ultimate control, you scale up or scale down the adventure as needed to be difficult yet suitable for your players, if your main Villian can only be hit by magical Arrows, and you don't have an archer, maybe change his weakness to being hit only by a magical mace which the characters have to first obtain before they can face him.
P.S. Might be a good idea to have your players have a extra character on the sidelines for if they die. Allways helps to keep the story moving along quickly incase of PC death or even Wipeout.