I'm fine with it. Running like cowards is choosing life over death. Bravest thing we could do.
In seriousness, we're talking about the continuity of a galactic society and multiple species. Bravely fighting the good fight to the last man is nice and all, but it doesn't do you much good when the end result is you being one of countless voices screaming in horror forever once you've been fused into a Reaper.
There's a one in four chance that we lose, and that chance comes down entirely to the decision of a marine who's likely suffering from a concussion and severe blood loss. With that in mind, I think that having contingency plans in place - such as, I don't know, sending people to survive in another galaxy - is a pretty good idea in hindsight.
Having said that, Andromeda does become a bit of a shaggy dog story for the Control, Synthesis, and high EMS Destruction endings. That's why, while I consider the high EMS Destruction ending to be the best ending to the trilogy, I think that the Refusal ending is the best ending when taking Andromeda into account, as now we are the last hope of preserving the Milky Way culture.