As a copy editor for a professional journal, how far should I go in adjusting the wording of an article? (It is important to note that the articles are generally written by people for whom English is not their first language)

I recently got my first article to edit, and realized very quickly how uncertain I was about how detailed I was supposed to be in my editing. The article was very wooden though and required a lot of editing to hold a professional English tone (to no fault of the author's, since English was not his first language). I am very good at editing and so had to settle on just going with what made sense to me, but I am wondering if there is a consensus or specific set of rules to follow. 

For instance, I always use the word 'one' to denote an inclusive general view in my essays (ie, "If one accepts the premise of John Doe, then yada yada yada...), but this author continually used 'we', which seemed odd to me. I couldn't tell if it was something that needed editing, or was an intentional stylistic choice. I decided to be conservative there and left all the 'we's, but would really appreciate some input.
I think a reasonable rule to follow when editing an accepted manuscript prior to publication is to make the minimum changes required to conform with proper grammar as well as whatever style guide your publication uses. (The latter might include, for instance, citation formats as well as the use of British versus American English for spelling.)

If there is ambiguity in editing possibilities, I would propose the change to the authors, but also, if possible, flag it as an "author query" to ensure that the change is viewed and a consensus reached.