It is unlikely Gadreel would've agreed to the procedure, yes. But if Crowley had gone ahead with it anyway, it would still have been torture. Now, I don't deny that it was for a good cause--to save Sam--but it's not benefitting Gadreel in any way, shape, or form. To him, it's still torture, and in fact, he does compare it to the agonies he endured in his heavenly prison. To compare it to a medical procedure seems misleading in this case, since Gadreel is the subject here, and not Sam.

The torturer's 'good intentions' don't matter nearly as much as the victim's perspective.