The same is true for stories. Stories that don't get a reaction from the reader have most likely failed what they were trying to do. The fact that this story progression has you feel something is an accomplishment.
But at the end of a story the reader / gamer should not feel SOOO sad, disappointed, cheated as a lot of people do. You cant just talk this "away". 
I was shocked, too when I saw the ending. Not only about the lost arm, but also about Solas plans for the world and his betrayal (I had NO Solas-romance). But: After a few time it was ok. The ending was hart, but great! It needet some time till I recognize this to be honest.
This is ok.
Bioware gave us the possibility to create our "own" character, to do something we can't do in reallife soooo good. This part of the game is very important for a lot of people. If you don't believe: Take a look on Nexus, how many cosmetic mods you will find there.
Bioware have taken our characters "away" and made a few unfriendly things with him / her (cut arm, lost mark, mentaly disstressed, I'm sure my Inquisitor have PTSD
). THATS OK! GREAT STORY, GREAT ENDING!
But now: Bioware, please, give the character back to the people, so they could try somehow to ... repair, clean up the mess as far as possible. And give a little choice to the people to do so. Of course: The Inquisitor will NEVER be the same again.
I repeat myself: Even in reallife you have the chance to choose what you want to do after sutch an accident: Chance nothing, wear a prothesis or even let your arm "regrown" (arm transplation: http://www.hopkinsme...transplant.html).
So the solution is just to give the people a little choice AFTER Trespasser what they want to do, with THEIR Inquisitor and the lost arm.
I'm VERY sure IF Bioware would do something like this, they would NEVER make something that could touch "really" the world .... I mean: They made the world, they know whats right and wrong.
"Bioware is the enchanter." 
NOT chancing the end - NOT chancing anything in the history, the world, the companions. Just: Giving a cosmetic choice AFTER the ending. Thats all.
If you are happy with your lost arm .... just don't care about. Make the choice that you don't want to chance something (or ignore the choice possibility) and nothing chances to you. Where's the problem? 
Please accept: For OTHER players OTHER game parts are important (as for you). The look of the character if VERY important to a lot of people / gamer / customer. You can't just say: "Ah come on, don't care about it. You are stupid / anti-social/ strange / a escapist or just superficial if you care about how your Inquisitor look like.