The main issue with that theory is that it becomes confusing as to why Mythal's betrayers would kill her. Its kind of like the whole Avatar thing. If you know that the person you hate is not bound by said body, then the thing you want to do is keep them alive but pacified in some other way.
Mythal speaks about the effort it took to find Flemeth, and it doesn't sound like it was an easy process.
As for his purpose- I don't think we're likely to find Fen'Harel having had cruel intentions for sealing away the elven gods. Not when we know the Pantheon was as corrupt as it was. Although it is certainly possible that, in order for the elven gods to be trapped, many other elves were caught up in the same snare in the process.
I suppose the transition would have had to be difficult to make Mythal so pissed off at her killer, she would NOT(edit sorry) have had to time to do the amulet/horcrux thing she did with Hawke at Sundermount thing with Flemeth. That wouldn't be clawing and crawling throught the ages would it?
I understand that there wasn't malicious intent in sealing people away, I mean to imply there was malicious intent for those he DID NOT seal away, or warn to sleep in uthenera(or however you spell it). Why would he leave so many people out? Let them rot away, and then just abandon as soon as he sees that they're suffering in the present day.