The ship needed a Valkyrie one way or the other right now, I probably would've gone with making a "new" one with her backup since they could. You still need androids presumably for running certain parts of the ship adequately, even if they'd be different than the original. Maybe since Homura can use the same ether stuff she'll be able to do at least some of the stuff Valkyrie was pretty much designed for? I also guess it would've just been a slippery slope into "I'm not the one you knew, but maybe we can start as new friends" transitioning into "Well they're basically exactly the same after all." This probably works better than that.