The latter. Elop has said this quite clearly, they don't want to split developer resources and complicate matters.

It's fairly sensible, though at least being able to run native C++ backend code would certainly simplify some porting efforts.

It's fairly stupid IMO, they acquired the whole Trolltech team with their Qt experience. Should they have coded Silverlight then? Result is that all good people already left Nokia.
It wouldn't have been too painfull to support both development options, it would just require advanced management skills, which were not available at Nokia.

Plus for Microsoft Qt would have been a nightmare. They only accept their own stuff on their platforms. They always did to that date.
I think this is the stronger reason for Elop to deny Qt.

Yes, of course they will have discussed that. Microsoft has a strong interest in keeping their development environment simple and straight-forward. Another reason is that Microsoft doesn't allow native code (for everybody) at this point, for security reasons. Qt isn't really a good match under those circumstances.

I wonder if SIlverlight and Windows Phone is really a long-term solution for microsoft. It feels like a transitional product, just like Symbian^3 and Maemo Harmattan, but microsoft is less open about its plans.
In a year Microsoft will probably release Windows 8 with touch support based on NT kernel not CE, support ARM chips, and much of the graphics effects seem to be HTML based (IE10), not Silverlight.

This positions Windows Phone at the lower-end of the smartphone range with "real windows" on higher powered devices.

Considering that all other "low-resources" OS-es have been killed (Newton OS, Palm OS, Symbian OS) because modernizing them would have been too much work, why would CE be in any better shape? I think it is much more likely that Microsoft is planning to kill CE, and that future mobile os-es will be windows NT based, they are just more secretive about it.