To upclock is to increase the maximum output of a hardware component. This typically increases the amount of heat the component creates, and heat is capable of aging and killing hardware. The more heat that is generated over longer periods of time, the more likely that the hardware will eventually degrade or fail.
The dimensions of the Xbox One hardware, and its ability to contend with heat, will define how vulnerable it is to hardware degradation. User care will also aid the lifetime of any piece of hardware. Consoles are specifically designed to be turned on and off often (unlike computers), so turn your console off when it is not in use. Give the console a 15 minute break once every 3 hours. Store the console in a spacious, cool area. Avoid placing the console on an object or in a space that retains heat, such as carpet. Do not place a console in direct sunlight, and controlling the room temperature via air conditioning or a fan is helpful as well.
No matter how poorly designed a piece of hardware is, if you can keep it cool, you will extend its lifetime.
A big issue I foresee with the Xbox One is that it's advertised as a general entertainment machine. Its "always-on" features imply that it should be always on--but should it? Should an upclocked piece of hardware be left running for such long amounts of time? I suggest that Xbox One owners pay close attention to how much heat the console produces when you are not playing video games. If the console generates as much heat with its cable television feature as it does rendering video games, I would avoid leaving the television on for a long time. Hopefully this is not the case! Hopefully the console goes into some kind of smart "stand-by mode" during television playback.
In the event that the Xbox One does have common heat issues, yes, Microsoft absolutely does have the ability to disable the upclock. This could be done easily via a typical firmware update. Not only do they have the ability to disable the upclock, but any game can be altered (downgraded) via software updates to suit the hardware.
Also note that, while the Xbox One may not be capable of true 1080p for some games, they may be able to cheese it. They could, like some current gen games, crop out part of the image that would have been rendered to make the game (fake) "widescreen". This would allow the game to be 1080p and non-upscaled, at the expense of having black bars at the top and bottom of the screen. This fake type of widescreen can often reduce processing load by up to 25%.