When you go talk to her and even Jaheira tells you, she's the reason that magic shield warding off the curse is her doing. What more do you need as a hint for the consequence of letting her get kidnapped? Even the dialogue from Marcus states plainly that he is here for her. Why wouldn't you be interested in protecting the cleric just earlier shown to be the source of the protection dome? Are people just not prompting the secondary dialogues available to NPC's?
I beat the fight before the hotfix patch on Balanced for my first playthrough, running a barb/druid/cleric/wizard comp. Marcus went first and still Isobel didn't come even close to dying because you have 3 characters who can apply CC to Marcus and Shadowheart with her Hellrider gloves applies 50% physical damage reduction to whoever she heals. Those gloves are pretty much impossible to miss at Act 1, since you get them for free for helping the tieflings. Shadowheart can also cast sanctuary so Isobel can't be targeted until she attacks, and on top if you throw an invisibility potion on Isobel, she can't be targeted by mobs either until she takes her turn and drops invis by attacking.
This is just one of the possible trivial strategies to protect her. You can also just burst out Marcus with a high level magic missile spell and giving Karlach a speed potion chug. He won't live past a single turn.
