Just stumbled upon this thread now while browsing some pages through old threads...
If you drank from the well and talk to Solas at Skyhold after, he is pretty upset. It seems to me he has reason to beyond just being a good guy... something more complex. If the essence of Mythal within Flemeth dies off, it most likely removes any bindings you have to her yet you are still imbued with the power/knowledge --- most likely knowledge and power they did not want to be in someone's hands that they no longer could retain control of.
Then again of course Bioware can go in any direction with it, but that is what stood out. Also the ending after the credits with Solas/Flemeth... the fact that he is stating he is in regret (that he should be the one to pay the price) could be all a part of a larger plan of his if he is afterall such a deceptive Elven God ---- so maybe this was his way of "staying on the good side" of Mythal overall while absorbing what power Flemeth had of Mythal..... since Flemeth described her bond with Mythal as Mythal being as much a part of her as a person's heart is to them --- it's not the entirety of them but it's necessary to live. Now with that in Solas' possession, he would be even more powerful.
Again, the Bioware writers could change any of this however they want down the road.. but with all of the information at hand it makes the most sense ---- doesn't mean it will be canon down the road but at this very moment it seems very logical.