While Logan was wondering why the hell his face wasn't healing, Mystique was having a ... much less lethal problem. With the pulse flowing through the area and shutting down x-genes, it meant that, while Mystique certainly wasn't losing any of her ability to fight ... she was losing her ability to shift.
And be blue and scaly. Which meant she was rather exposed at the moment. It didn't seem to bother her too much (she walked around naked as a rule, after all), but ... it meant she looked human, and wasn't that was unfortunate.
Wolverine had slowed down considerably, making it easy to dodge before jamming the pipe up under his jaw.