Eh? Rooting phones is not a big issue for mobile phone providers (outside of MS and Apple enviro's) and in fact many see it as a way of selling more handsets. Look at Samsung who recently supplied Galaxy S2 handsets to the Cyanogen team so they could port CM7 to it, then look to HTC who confirmed they would unlock the boot loader on their new phones. Publically the phone manufacturers might not be seen to like phone ROM cooking (I avoid the use of the term hacking for the obvious negative connotations of the word) but certainly the Android suppliers like HTC and Samsung love it. It makes their device far more saleable to the people who don't like the idea of not being able to do what they want with it how they want and whilst Apple might publically moan about Jailbreaking it's massively helped with hardware sales. The only negative I can think of is for the app makers who rely on adverts for their free games when rooted you can use a custom HOSTS file and block all the adverts, apart from that I cannot think of a serious negative that would upset Google, HTC, Samsung and the like but I could easily be wrong...
You only have to look at Modaco and XDA to see how fast development is happening for these 3rd party ROMs far far faster than the OEM will ever commit to and in fact many of these ROMs make the device infinitely more usable - Proxy support Android i'm looking at you!
Whilst I am still running a stock ROM on my S2 I am running a custom kernel and rooted which allows me to do things I would not be otherwise able to do and makes the phone much better for "me".
Samsung and HTC at least recognise that and realise it helps with sales otherwise they would not do what they have done.
TBH this UEFI secure boot thing is nothing more than the latest shot across the bows and I wager it will come to nothing previous examples:
PIII unique processor serial numbers - Outcry and option to disable added to BIOS options
TPM platform - What happened to that?
MS need to look at all these secure platforms and see what's happened to them:
Xbox - hacked
Xbox360 - hacked
PS1/2/3 - hacked
Apple OS X hardware check - hacked
Blu-ray secure platform - hacked
HDCP - hacked
In short even if they do implement this and ram it down our throats (which won't happen due to Linux etc crowd fighting it) it'll be broken in very short order