What you are suggesting is cold setting chromoly alloy steel, which shouldn't be a problem if the extension doesn't have to be twisted very much to get the clamp area back to level, but there are a lot of details that may complicate things. Is it a quill stem for a threaded steerer, or is it threadless? Is the handlebar clamp area part of the stem, e.g. forged as a single piece, or is the handlebar clamp welded or brazed to the forward extension?

How about posting a detailed photo? How many degrees (angular) is the clamp area twisted out of alignment?