Yes that one quest was a quite big hint that the soul is still there after death but the problem is, that this is quite the contrary to what the main quest told us about it. I don't have any dialog I can post and I only now it about the German version but there is one point in the story where the Scion discuss the way the afterlife works or better the way that the Ascians escape their fate.
In this they showed that the soul becomes part of the great lifestream and maybe one day parts of it will go back and be reborn as another person. Later also we have the situation with Y`shtola who was in the lifestream for a short time but she said that she had a hard time to keep herself together.
These two things show me that this version of the afterlife does not include any kind of heaven. And that its quite likely that anyone that dies loose their own self and be united with the stream only to maybe one day be reborn again as a completely new person.
The alchemy quest line was quite surprising for me because it showed something different from that and I am not sure if this was done to show us that maybe there is more to it than the Scions know or if it was some kind of mistake from SE.
If the version of the Scions is true than its even more harder for me because in other games where they keep it ambitious (which I like the most

) you can make up your own version but in this you are straight told what is going on after death.
Still even if in some kind of strange way they have some kind of afterlife it would still mean that we as the players wont truly see him again which is still kinda horrible for me..
Now onto the rest of your post
For me a death done only for emotional impact feels always cheap in a way. If the character dies so you can defeat an evil or if their death is the only way to let you life (an in this situation we could and should have defended ourselves..) or if their death truly changed the story than I can at least accept it. But death just so that we can have a personal reason to go after someone or that they can show how bad war is or to just to have us feel some emotional pain leaves a really bad taste..If he would have taken an enemy with him or if he like Moen, gave is aether so that we could defeat a Ascian for good than it would have been not that harsh. (But still very sad T_T) But killing someone of to create a feeling of vengeance and hate for another character is really the easiest way to do that and with that feels kinda cheap

.
[And yes I know that a lot of people die without reason in the real life, but I don't want those deaths in a video game or book. I am mean how bad would it be if for example Aymeric dies because he slipped on the stairs or Thordan died of a heart attack thanks to his old age xD]
Why do we truly need such a personal reason to go against Thordan? Wouldn't the threat that he and his knights pose as primals not be enough? Just the thought that if they will win that they would slaughter countless innocent dragons and people alike should have been enough to get such a feeling.
We never needed that much of a reason before and just because your character may feel a little bit annoyed to do everything other ask for them does not mean that we wont go against primals and other big threats to defend innocent people. Its the ones that use us for things that they easily could do themselves or that risk their lives for something small with the knowledge that we will save them, that annoys the WoL.
I can understand that his death was the beginning of change in the characters of his brothers and that we one day might remember him and that it will help us. But for me it would have been better if he had been quite injured which would have him helpless for the whole 3.x story which would have been a chance for his brothers to shine. Maybe they could have injured him permanently so that they would have a reason to not include him that much anymore but he would have still been there so that we could visit him. This could have given him some new character development too.

This is probably harder to write in the story than a character death but it would have given the devs the chance to include him in other things in the future outside from all the fighting like events.
Maybe I am just so sour because we already lost some dear people and I fear we will loose even more. I am just not a fan of death especially if there are my favorites and maybe I am also still a little salty that we at the same time did not loose a single Scion after all that happened at the end of 2.55 but that we had to loose Haurchefant and Ysayle instead

. Why always the characters with the most development? T_T
So yes deep inside I would have no problem if he is somehow able to be alive again. Maybe after a really long hard quest line or maybe he was chosen by the Mother Crystal to be her version of the Ascian. (Yes I know it quite impossible but one can dream right? xD)