You can easily delete the skills and classes in the database so they are no longer an aspect of the game. Every new project will re-fill these default skills and classes but you never have to use them. In fact, you don't even have to allow the player to have access to the in-game menu if it would get in the way of your story game. There's an option on Tab 3 of the Commands menu under the heading of 'System Settings' that is called Change Menu Access- that means your players won't see their stats, equips, level, items, etc. so keep that in mind before you do that. But you can always make every item a "Key Item" and rely heavily on the Select Key Item command on Tab 1 (it brings up a list of the items marked [key item] to choose from).
If you wanted battles, you would still need at least an Attack skill so they can do some damage- it's always the very first skill so as long as you keep that one and default all the weapons to it, you should be fine. But if you want different characters to have different weapons and different attack animations, you would want to use skills. However, if no battles are in the game at all then there is no need for the skills.