Disclaimer: I've never played any Mass Effect game. I have played nearly every other Bioware game, so I feel like if I squint and picture my PC and his/her companions in shiny spacesuits with different skin colors or headbumps, I sort of have played it, but I realize that probably really doesn't count.
Anyway: as a semi-detached bystander, my view of the situation is this:
Bioware has a reputation for making games with in-depth stories where the choices you make matter and affect the ending. Most Bioware games have endings that change depending on how you play it. They have firmly planted in the minds of their fans that their choices matter. So if you suddenly, after years and years and years of establishing this reputation, in an already established series that has also reinforced this idea, decide not to do it like this anymore, it is at the very least very jarring. At most, it's a very poor design decision to throw at a loyal fanbase without warning--and may sever the fanbase in the long run for little reason.
That said, as much as I like the mutable ending idea to a degree, I agree with Yahtzee that it can be frustrating to not have a canon ending to some games. In part, because it takes away a sense of closure, and you never feel like your end "counted." In part, because if the game with the mutable endings ends up having a sequel, the developers then have to pick the "right" ending to carry on from. Suddenly one kind of ending became canon, and if your game ended differently--again, it doesn't count.
I can kind of see the idea of if you want to end a franchise, such as Mass Effect, you might want a non-mutable ending so no one bickers about what "canon" was. But a) gamers will bicker no matter what you do, and b) a solid ending in a mutable, your-choices-matter story is in itself inconsistent. Maybe if Bioware wants to take a route where stories have more solid endings in future, that's a really good idea--they just shouldn't have started with Mass Effect 3.
And THAT said, I agree with the article that changing the ending officially could set a bad precedent -- especially since we as gamers will whine about everything we don't like to the point we will make up something not to like if something is perfect; we suffer from massive cases of "unpleasable fanbase" on a regular basis.
On the other hand to THAT, though, there are actually existing precedents to changing endings. Fallout 3 comes to mind. The original ending to Fallout 3 handwaved past some major plot/logic holes to force your character to make a noble sacrifice (maybe this sounds familiar). Or to force a specific NPC to make a noble sacrifice. But the game itself had established possibilities for reasonable alternatives. When enough players vociferously pointed this out, Bethesda changed the ending to the original game when it published one of its DLC add-ons.
So this HAS already happened. And Bethesda specifically established a precedent of "we'll fix this when the DLC comes out" (though I think they patched the original game at the same time). Still this leads to...
A sinister thought--could this even have been planned? Would the possible new ending be a patch, OR do you only get the new ending if you buy DLC? EA LOVES to nickel and dime its customers with downloadable content (one of the reasons I in fact stopped buying Bioware games). Is it possible they're testing and seeing customer response--don't like the ending? How much are you willing to pay for a new one? Are you willing to pay for other added choices as well?
I hope that last thought is a bit extreme. But it will be interesting to see, if Bioware does rewrite the ending, what form of the delivery of that ending will take.