I agree, my first playthrough was really rough because of this. It was also before Isobels HP and AC were increased, so my Rogue got 1 turn before she was KO'd and taken. It felt awful, especially considering the consequences. That whole playthrough was just crippled and I missed out on SO MUCH content because of it.
Anyway, there's a super easy way to deal with this (one low level spell) and other easy ways to deal with this, IF you get initiative fast enough

I totally support giving players at least one extra round before she is taken away and the failure cutscene starts. I suggest this: when she is knocked out, Marcus gives orders to his allies and casts a crowd control spell / uses shove and attacks on the players to make him picking Isobele up next turn easier.