When I first read about this I was immediately excited but now that I've given it some thought I can't help but wonder why it would worry Canon or Nikon? Sure, Sigma makes a few really good lenses but the phrase Oh I wish I could swap from Canon to Nikon but cant because of my Sigma... is something I've yet to hear a single photographer utter… ever.
Well, the thing about both Nikon and Canon is that their main strength is their
system, rather than a particular product in a system. Part of the success of a system is the fact that you accumulate lenses over time, which usually locks you into a particular brand, since it rarely makes sense to sell off all your gear just because Nikon released a D800 (and Canon is late to the party, maybe by about 2 years this time round), for example.
So Sigma's new mount-switching announcement is not that significant to photographers with bags full of gear, but it is definitely something that will (or at least should) affect your decision if you are just starting to assemble your kit. Your system could actually be planned around Sigma lenses, while remaining brand neutral w.r.t. the body.
Sigma's move certainly makes it harder for both Nikon and Canon to predict expected future sales of both bodies and lenses. Given that they have been accumulating obscene quantities of old stock (I still see 600Ds, D3100, D5100 on sale every week!), i.e., they are already struggling to produce accurate sales forecasts, it seems reasonable to suppose that Sigma just made things even harder for them.
This may not affect the pro market as much (as you pointed out regarding the lens choices at the exotic prime end of things), but it certainly impacts the enthusiast market, where sales volumes are arguably much larger.