Using Tweak Everything, parachutes no longer deploy instantly and risk ripping the ship apart. Thus it is no longer necessary for engines to fire during parachute deployment. However, MechJeb doesn't recognize this and instead continuously fires the engines, even after the chutes have opened, until the ship starts going upward and breaks the chutes.
Is there a checkbox to disable this feature?

I think this is no longer relevant.

I will have a look after 1.0 is out and I made the required patch.