If you are running any form of Operating System, then what you are proposed goes against the whole principle or modern multi-tasking operating system. Graphics works involves more than playing video or 3D graphics or anything else in between. The operating system has to manage the display, so you disable the APU use of video, how is the operating system display manager/compositor suppose to display your computed result onscreen ( and by that I mean something as simple as an X terminal )? Are you going to be doing a headless system? Whatever concerns you may have about being the sole user of the APU compute capabilities may be unfounded. I would proceed and not worry about such trivial issue and save that for when you actually experience performance issues running your compute load.