Many questions on SO say "Windows developer guidelines" or "windows design guidelines" say that you shouldn't write temporary or program data to the Program Files area, but as far as I can tell none of them actually link to a piece of documentation that says as much. Searching the MSDN has yielded me no results. Windows will make the area read-only, so it can be enforced by the OS, but that doesn't mean developers didn't try to write there anyway (e.g., when porting older, XP and earlier based programs forward.)
I realize that it seems odd to ask about it this late into Windows development (since, as a commenter below pointed out, has been enforced by the OS for more than a decade), but a document that says so is sometimes necessary to satisfy people.
With that in mind, Does Microsoft have a document published stating we shouldn't write application data to the Program Files area, and if so, where is it?