Yes, when instrumenting, the profiler is going to modify your code with additional instructions to gather and track the necessary performance data. You'd never want to distribute an instrumented version of your assemblies, and you wouldn't want to use instrumented assemblies for debugging purposes (as critical sections / race conditions / etc could certainly behave differently given the additional instrumentation).
That being said, instrumentation can be very valuable for the goals profiling is meant to address. By gathering actual data and isolating expensive operations, optimization efforts can be focused appropriately and the results can be measured accurately - avoiding wasted time, increased complexity, reduced maintanability, and all the other problems associated with premature optimization.