Should being morally good in all instances lead to the "best ending"?

In this case, the playing public is simply parroting the morality being "taught" by the game.  The devs decided for us that this was a scenario where one could possibly justify sacrificing a large number of innocent civilians; but the actually "goodness" of that morality is still debatable.  Shepard doesn't really know that the Alpha Relay is the only opening the Reapers have into the galaxy.  He/she has no actual way of knowing that destroying that relay will buy them any significant amount of time... all he has on any of that is Kenson's word.  The artifact's proof is that the Reapers were planning to come through that Relay, being a Reaper controlled artificat, it is not logically that it would reveal that destroying that one Relay would completely derail the Reaper's plans for months.  Shepard is literally throwing away the lives of 300,000 Batarians on the sole word of a totally indoctrinated individual.

Shepard fumbled the ball when they failed to set up a plan for reinforcements the moment Shepard confirmed Kenson was free of the prison.  Instead of going to the base alone with Kenson to get proof, Shepard should have been conferring with Hackett while in the shuttle with her.  It was not Shepard's decision to make at any point in time.  Heck, Shepard wasn't even part of the Alliance.  It certainly wasn't Kenson's decision either.  She obviously wasn't acting under orders from the Alliance.  She's a rogue operative taking matters into her own hands.  Hackett is also complicit... letting his friendship with Kenson get in the way of his doing his job.

And yet they go out of the way to introduce and Alpha Relay that when tuned right will connect directly to the Citadel Relay. Information Shepard is explicitly told. Also explicitly told is that this is a unique one of a kind Relay because it functions as both short and long range Relay.

The entire basis of the Mass Relay system is that the space between worlds is so long that it would be the equivalent of sailing from England to North America in the 1400's.

Which are valid words given she is a respected scientists and the Alliance wouldn't be chasing ghosts in the ass end of no were unless there was valid proof. While Anderson and Hackett have been willing to give Shepard the benefit of the doubt they are not the sum total of the Alliance command and it wasn't either of them that sent Kenson to the system nor started to provide them with the resources needed to build the base.

Why did the artifact reveal any of that? It has been a while since I played the DLC but I do not remember the artifact telling Shepard that destruction of the Relay would derail the Reaper's plans for months? The only one I remember mentioning anything about delaying the Reaper invasion is Shepard because it would force the Reapers to have to reach the next Relay before they could start invading which would by some time.

It is based on the data she gathered before indoctrination and the fact the artifact and the entire base of indoctrinated individuals tried to stop him from blowing up the Relay. The very same indoctrinated people who behaved perfectly normally and supported Shepard right up until he tried to do something that would negatively effect the Reapers. If blowing up the Relay would have done nothing to Reaper's invasion then there would have been no reason for the indoctrinated staff to lash out at Shepard. It would have been far more useful to help him blow it up then be pulled back into the Alliance to infiltrate key strategic areas and then betrayed them during the Reaper invasion to help cripple the Alliance against the Reapers.

My point was exactly that the artifact did not likely reveal that destroying the Relay would derail the Reaper plans.  Only Kenson's word supports this theory... and she's clearly crazy (indoctrinated).  Even before indoctrination, Kenson is off the reservation... taking the decision to destroy the relay into her own hands and it's not her call to make.  She's the leader of a rogue group, looking to destroy a star system.  In many circles, they'd be labeled as terrorists.

At any rate, regardless, it's not a decision that was ours to make in the game.  It's a decision imposed on us.  I find it unusual that people who will complain about the endings imposing a "genocidal" decision on the player have nothing to say about this one... which is clearly imposed on us.  In the end, they're games and fictional stories... not a means to "teach" morality.