The current rule is something like 1,200/year. There are about 143,000 bald eagles in the US. The 4,200 number is set at a level which they think the species can sustain. I don't know why bald eagles would be more likely to be killed by turbines, but apparently they are:
http://www.fws.gov/midwest/wind/wildlifeimpacts/index.html
"Not all bird species are equally vulnerable to wind turbines. Eagles appear to be particularly susceptible."
Not all birds fly the same way, in the same regions, at the same altitudes. Balds eagles tend to soar and hunt in places we like to put wind turbines. Small birds tend to move smaller distances, often in about 100m around a water source.
I don't see any reason why bald eagles would be more likely to be killed by turbines than other species of birds. If only 0.01% of birds are killed by turbines, then they would only kill 1 bald eagle a year out of thousands.
Regardless, this is more of a reason to invent solutions for repelling birds from turbines. Maybe we could come up with noises or lights that repel them. Or drones, or a water cannon robot. But I'm not certain it's even an issue.