Starting in Sytist 0.7.7 you have the option to replace photos. There are a few ways to do it.
Under the thumbnails when viewing photos in the admin, there is a new Replace Photo icon.
When uploading photos there is a Replace photos with same file name option.
With this selected and you are uploading photos directly to a page, this will replace any photos assigned to that page with the same file name. It will not replace photos not assigned to that page if there is any by chance.
When uploading photos directly to the All Photos section, then it will replace any photos with the same file name in the system.
You can also replace download photos on an order in the Manage Photos tab when viewing an order.