Choice not always good
It's a pretty solid principle that giving non-technical users too many choices isn't always a good thing, let alone giving them exactly what they ask for.
If every new way of doing things was implemented as a choice between new/old ways, nearly everyone would play it safe and the new ways wouldn't get used. If your company believes it really has an improvement, forcing users of your product to use it isn't a terrible plan - they can always use an alternative product if your vision turns out to be wrong.
For instance many people here have said things like "I prefer ribbon now but I initially hated it"... if it was an option those people would have turned it off and never found it actually was better (to them).
Also, didn't Outlook get threaded functionality in 2010? I'm sure I read it somewhere, maybe on El Reg actually.
Conversation threading is a feature it _is_ reasonable to make optional, but the principle of making _every_ innovation optional is not, your app will end up too complicated for users to manage all those options and they won't ever give new innovations a fair try.