The movie goes to great pains explaining the notion of experience versus reality within the context of 'The Matrix'. As such we know that there is literally no pill; they do not exist. I guess it can be thought of as a 'sudo' for the trace program? Either way, I don't believe anything is actually being initiated from or by the pill as we understand things. The operator is the one actually executing the program. Why would the operator choose to run a trace program and put someone to sleep? Just because Neo could potentially decide to take both pills?