Actually the prettyPhoto plugin (that came with the theme) is only designed to work for the Portfolio template of the theme, it wasn’t designed for the WP gallery or anything else. If you have other plugins/areas of your site that use prettyPhoto it should still work fine as the theme’s version of prettyPhoto is only loaded on the portfolio template and not other areas of the site. So there shouldn’t be a conflict.
You can take a look at the Tutorials if you want to remove the prettyPhoto effect and have it link to the post instead – https://appfinite.com/tutorials/how-to-remove-the-prettyphoto-slideshow-effect/