The collision warning should never break you so quickly unless you are about to get into an accident, at which point who cares if you stall it just saved your ass from crashing. Sometimes my parking sensors go off during slow rolling traffic which is pretty annoying, and I have had my collision warning go off and stop the vehicle when I quickly applied breaks in a slow rolling traffic scenario when I'm pretty sure I could have easily stopped on my own. It has never suddenly tried to stop me from 60 for no reason though (which is when you would have a problem needing to downshift instantly to avoid a stall).
As for the ACC and manual. As I have said in my previous post, pressing the clutch and shifting does not turn off the cruise control. So, it actually works quite normally with 6MT. Say you are on the highway with ACC set to 60MPH and you are in 6th gear, but then you approach a guy going 45. ACC will begin to slow your speed down to 45 MPH, as it slows you down, you realize you are slowing down, then you downshift to 5th, and it will continue to slow you down/hold speed/or accelerate depending on what the traffic in front of you is doing. When the slow poke gets out of your lane ACC will begin to increase speed to 60MPH again, and you can shift back into 6th. Throughout that scenario ACC is never disabled.