For me I think Command did the absolute best they could - Because they weren't even trying to do what we think they were trying to do in the first place.
I think Command was trying to get the ETAK plans from the NTF, not just destroy the Iceni outright and crush the rebellion. If so they would probably have deployed the Colossus sooner. In fact, since Epsilon Pegasi really had nothing to do with ETAK at all (I guess there was no Ancient technology for the NTF to plunder), Command decided that they should just end the Epsilon Pegasi invasion there and then, instead of farting around and letting the NTF get Ancient records like they did in Deneb and Alpha Centauri.
Makes no sense, I know, but that's what I think.