I agree with you about the eluvian being the only doorways to the Black City prison.
And beyond the Elgar'non murdering his wife in a jealous rage theory, perhaps Mythal was murdered by her slaves as she slept in Uthenara. Yeah, just another thing we can pin on Fen'Harel.
If you want to get really stretchy with figurative meanings (and artfully avoid Solas x Mythal awkwardness for your Lavellan) here's one possible interpretation:
Solas takes up arms against the status quo in ancient Arlathan. He's alone, intially, but eventually 'woos' Mythal to his way of thinking. She leaves her closest allies, joins him in his rebellion, and is killed. So... duelling ideologies are the actual conflict reflected in the husband/lover dichotomy of the various myths.
AND THEN THE WOLF IS ALL OURS
(did I say that out loud?)
Anyway, sketchy support for any of it, aside from Flemythal's general non-interference in modern Thedas and apparent total lack of interest in developing a fawning legion of slave-worshippers. I think after the last few millennia, she's done with the whole 'making the world better' crusade, if she was ever really on board in the first place. She just wants people to leave her the hell alone while she plots revenge.