If you don't want the workflow to run every time it is edited, then why is the workflow set to run on edit? You have to decide how the workflow is supposed to work. Should that setting be changed? When do you actually want it to run?
Anyway, if you need it to run on some edits but not all, then put a step at the beginning of your workflow that has a condition or set of conditions. Check a field (maybe a new field with flags set) and based on that field's flag, tell the workflow to step or let it continue. You just have to add logic. The workflow will still always run, but you can stop it before it does anything.