I suspect it's mostly just their usual ruthless approach to winning. Froome is a better climber than Wiggins and an only slightly worse time trial rider. This Tour is more weighted towards climbing than last year's wet dream parcours for Wiggins. So Froome is more likely to produce the goods. So he's the planned leader. No sentimentality. No loyalty. Just numbers.
They also probably figure that Wiggins, if he has last year's form, can probably win the Giro and two GTs are better than one. Plus, there may be an element of a longer term calculation: Froome is five years younger than Wiggins, and therefore backing him can help them bring in wins for longer than backing the older guy.
It may also be that Wiggins has changed his mind about his goals since it started to look more likely that Contador may not be the force he was. He might not have thought he could realistically defend the Tour back when the GT split with Froome was first talked about, but now thinks he can. Which would be the sort of thing that would cause a lot of friction on a team.
