Set Telltale's Game of Throne to display prompts for PS3 controller on PC?

How can I change it to PS3 prompts?

You can't.

The overwhelming majority of games are designed for XBOX controller prompts.

Why, you ask? Simple, a majority of people us an XBOX controller over a PS3 controller because there are officially supported windows drivers and the Games for Windows certification program requires XBOX controller support.

http://msdn.microsoft.com/en-us/library/windows/desktop/ee417691(v=vs.85).aspx#tr_1_4

Requirement
Games that support gamepad controllers must support the Xbox 360 Controller for Windows using the XInput API. If DirectInput peripherals are also supported, then DirectInput can also be used. However, XInput must be the default API if an Xbox 360 compatible device is used. All references to common controller triggers and buttons must use the Xbox 360 names. See the Xbox 360 Common Controller for Windows Terminology list for details. Controller vibration must be turned off when the game is in a paused or suspended state. Mouse/keyboard control cannot be fully disabled at any time. At a minimum, an option to return to game menus must be available.

Rationale
This requirement gives gamers freedom of choice to use either the Xbox 360 controller or the keyboard and mouse, depending on which input method is more natural and intuitive interface.

Additional
Information This requirement does not apply to games that use only the mouse and/or the keyboard. We recommend that menu navigation be implemented to use the widely accepted standard controller buttons: A - Accept B - Cancel Start - Accept or pause Back - Cancel, back one screen or up a menu level

The Final Fantasy games are one of the few titles that will have in game PS3 controller prompts as Final Fantasy was/is primarily a PS title.