Very good question!
Not sure will this work in your C# addin, but with Excel 2010 Application object model, you can use Application.CalculationInterruptKey to stop interruption on data calculation when a key is pressed. Not tested but this can be it.
Apply this at beginning of CtrlAltF9:
Dim lKey As Long
lKey = Application.CalculationInterruptKey
Application.CalculationInterruptKey = xlNoKey
Then at end of calculation, reset it to what it was or change it to default xlAnyKey.
Application.CalculationInterruptKey = lKey ' Or xlAnyKey
If you have other event triggered Subs, you may want to add lines about Application.CalculationState such that it won't make changes until Application.CalculationState = xlDone
.
Hope this helps.