There are loads of ways of approaching this, I think I can make sense of two.
1) The wish isn't affecting the golem as much as it's affecting reality. The SRD says, in the description "By simply speaking aloud, you can alter reality to better suit you." So, one could argue that what the wish is doing is affecting both the way that magic affects golems, and this particular golem.
2) The wish changes things so that the person doing the wishing becomes the person who created the golem, and this creation included placing some degree of control in the hands of the creator.
In both cases, I'd go with a duration. And, with the second option, I would have the "history" fix itself when the duration expired.
Dave