Without getting into the ins and outs of feeding stunned prey, I will say it sounds like you may have a shy eater. Given that, going forward I'd let the snake do what it does best once the rat's been introduced into the tub. Supervision is recommended, intervention can throw a shy eater off stride.
Bottom line, your snake did finally eat, so what you did wasn't the end of world.
Please feel free to continue the previous debate. I would like to mention however, while some practices may be standard, nothing is really one size fits all. Not all keepers do things the same way, and that doesn't make it a crime....may not be how YOU would do it, but doesn't make it a crime.