What's so inherently bad about pain?

The proper way to prove that pain is bad is proof by induction: specifically, hook an electric wire to the testicles of the person who doesn't think pain is bad, induce a current, and continue it until the person admits that pain is bad (this is also the proper way to prove that creationism is false, or at least the most fun).

Is it morally questionable to run a piece of control software for a cleaning robot, that has a "const bool in_pain = true;"?

This is getting into the subject of qualia, which I freely admit to not understanding. But I'm pretty sure I have some, and I'm pretty sure they're harder to produce than a variable with the label "pain".

With his intelligence intact, he can still be valuable to us, and depending on what he did in the past, we may be in moral debt to him.

I'd guess from this statement that you're either not a consequentialist, or you're some exotic type of consequentialist straight out of Alicorn's syllabus. If you clarify exactly what your moral theory is, I can give you a better estimate on how likely we are to be talking past each other because we have completely different premises.