It's important that NCrunch keeps itself up to date with the changes in your solution, so I'm assuming you mean that you want NCrunch to only run builds and tests after the package update has completed?
The tricky thing here is that at present, I don't know of any way for NCrunch to be aware that Nuget is performing an update .. it simply sees the changes that result from this update, then reacts to them.
Is the sequence of changes causing the engine to fall out of sync?