No system in the world can stop some outside forces from inflicting change on you in small or big doses - I recently received a load too. That "queasy feeling" is no stranger to a lot of people.
Don't blame GTD for those people's behaviours, and don't blame yourself.
Pdaly is right - collect like crazy and just deal with the day as it comes up. As long as you still process about once every 48 hours your GTD should tick over just fine in the background.
Once it's settled down, I suggest a higher level weekly review, taking in your horizons of focus, and see if you want to build a little more "slack time" into your life. That's no use now, but something to contemplate at some point if these kind of changes at work are inevitable.