Because of this 'extended control' spells such as Mordenkainenen's Disjunction, Greater Breach, Lesser Breach and Lower Spell Resistance now actually do reduce a target's Spell Resistance score. NWN2 by default intended this feature, but it never worked. Spell Resistance reducing spells do not stack with one another and as a general rule a higher reduction will override a lesser reduction. There is one exception to this rule however: Assay Resistance does stack with all other spell resistance reducing spells. Reduction of spell resistance is not visible on the character sheet, just as assay resistance is also not in the normal game.
The new Spell Resistance mechanic also facilitates Spell Turning type effects. This feature has so far not been made publically available for balance reasons. A Dungeon Master in a good mood might be kind enough to award you a scroll of Spellturning if your character makes a good case for it. Archmages also have access to the feat: High Arcana Mastery of Counterspelling, which lets you turn a counterspelled spell back on the caster.
Custom spell resist mechanic curtesy of Rasael, testing by the Quality Control Team.