Let me put it to you this way: what's done is done!
I've pruned my autos (they're all I grow) with no ill effects... in fact, the ones I'm currently growing I wish my pruning HAD stunted them because they're WAY too big. If you choose to prune, do it for a reason - for example, to allow more light to the lower bud sites or to get more air flow through the plant. Start out cautiously - only prune a few leaves (fan leaves that are growing toward the center of the plant or that have a purplish stem are great candidates)... then let the plant be for a day or two to see how she reacts. If there's no obvious harm (i.e., she's stopped growing or some other major difference), and you feel you need to prune some more, go for it. Some strains will take it, others will put up a fuss...
One thing I DO know about autos is they really and truly do not like to be transplanted. If you grow in a fabric pot and think you need a bigger pot, all you have to do is get that bigger pot, fill the bottom with soil so that when the smaller pot is placed inside the soil is level with the top of the bigger pot and then fill soil around the smaller pot... the roots will grow through the fabric and into their expanded space without any of the stress transplanting causes.