No reason for a monitor to question protocol, but certainly reason for a human being to.

It wasn't in the nature of GuiltySpark to feel remorse, or guilt about activating Halo, for him, it was simply a procedure that had to be done. But for the Forerunners, imagine what it would've meant to them to knowingly activate a device that would extinguish life throughout the Universe. Not something I'd do lightly, and not without asking a couple people about first.

I think the Forerunners felt guilty for having created such a device. They thought it necessary, but felt guilty none-the-less.

Think about the names of the monitors: Guilty Spark, Penitent Tangent... all efforts at giving an otherwise unfeeling entity "guilt" as well. A personification of sorts... so that while the monitors themselves aren't full of remorse, you know the people who created them were. Which I think is what the original question to the Master Chief by Guilty Spark was meant to bring up - the fact that the Forerunners didn't want to really use the weapon to begin with.

Of course they didn't, it was a weapon of last resort for a reason. They had no other option.

He may not be 343

I agree with HardwareHeretic404 it couldn't have been 343 Guilty Spark. The fact is that he isn't re-activated for another 500 years or so and the events are taking place now in 2007.

AdjutantReflex might not be a monitor, but he had a role in the Forerunners plans for earth/ark. Perhaps instead of a monitor he was more of a clerk or provided information to the reclaimers.