In addition to zeroing out the alternate engine, they also cut 10 production aircraft from the FY 2011 for failure of the program to execute per schedule.
This implies to me that neither cut could have gone through on its own, but together, both those who have concerns about the JSF, and those who don’t want the engine got enough of what they wanted to support each other.
Meanwhile GE/RR is ramping up efforts to reverse this decision, noting, among other things, that the budget numbers that the Pentagon is putting forward on the F136 engine are sketchy at best.