Hi Michael,
You're absolutely correct, the debug tools do increase the load and as well as throw off the timing in your real-time applications. However, what your viewing in the RT System Manager is a representation of only your application itself, i.e. RT 7.1 shouldn't be adversely effecting the CPU load of a period of time. (But if you think otherwise, than perhaps there is an OS problem that we need to know about!)
In general, if you trying manager your RT application at the thread level the right tool to use is the LabVIEW Execution Trace Toolkit:
http://sine.ni.com/nips/cds/view/p/lang/en/nid/13746
By the way, I'm not sure how much overhead the RT System Manager occurs, but it certainly has some overhead associated with it.
Regards,
Jeff M.
Applications Engineering
National Instruments