Exactly, I mean, just look at the situation from the council/galactic leader's pov:
If my only hope is a magic super weapon, that nobody knows how exactly works, which came from a guy crazy enough to blow up a Batarian system... The first thing I'd do would be starting to look for plans B to D, and fast.
It's also possible they didn't want to insult Shep or undermine the morale of the war effort by revealing that some people were actively preparing for the pay possibility that the Commander might fail and everyone would die.
Shepard still had to be the big great galactic hope, but it makes sense that people didn't want to rely on hope and an untested alien blueprint alone.
Someone pointed to what the asari councillor said after Thessia, that she needed to set plans in motion to guarantee the preservation of civilisation. It'd be really cool if that ends up being a reference to an ark contingency project, and it makes sense that they'd be panicking after their home world fell.