All keyboard shortcuts can be modified via menu EDIT->KEYBOARD SHORTCUTS. Ctrl+S is usually assigned to "Save", but be removed here.
Try to assign it again and see if it works.
It's normal for you to see the Save As dialog the first time you open a legacy file in a newer version of ID, or the first time you save a new file or a .idml/.inx file, or one created from a template (and even some files that come in on removeable media because they are marked Read Only), but if subsequent uses of Ctrl + S are bringing up the Save As dialog it's more likely a prefs problem than a problem with the shortcut set (but it never hurts to check, and that's the first thing I'd do). If it's not the shortcut, next step would be to replace the prefs. See Replace Your Preferences