TDRs (the 2s timeouts you see) are a reality of using a resource that is shared between rendering the display and executing your compute work. The OS protects your application from completely locking up the display by enforcing a timeout. This will also impact applications which try and render to the screen. Moving your AMP code to a separate CPU thread will not help, this will free up your UI thread on the CPU but rendering will still be blocked on the GPU.
You can actually see this behavior in the n-body example when you set N to be very large on a low power system. The maximum value of N is actually limited in the application to prevent you running into these types of issues in typical scenarios.
You are actually on the right track. You do indeed need to break up your work into chunks that fit into sub 2s chunks or smaller ones if you want to hit a particular frame rate. You should also consider how your work is being queued. Remember that all AMP work is queued and in automatic mode you have no control over when it runs. Using immediate mode is the way to have better control over how commands are batched.
Note: TDRs are not an issue on dedicated compute GPU hardware (like Tesla) and Windows 8 offers more flexibility when dealing with TDR timeout limits if the underlying GPU supports it.