I think "simply" as a synonym for "instead" is part of the problem here. "Instead" is probably the better option in most cases. For example, in the case you gave, "instead" is the clearer word choice because it clarifies that you are (only) presenting an alternative course of action, rather than offering a value judgement on that action. Similarly, "only" is generally better than "just", because again, it tends to be less loaded and more explicit.

This won't be applicable to all writing - writing for entertainment or to make an argument will look very different - but in technical writing, clarity is key, and words like "just" and "simply" are usually less obvious than their "only" and "instead" counterparts.