I thought I was the only one left bothered by that. Still, that problem originated in season three, not season five--the writers dropped that hot potato almost immediately. Doakes hardly gets a mention (much like the Bay Harbor Butcher) after season 2.
And it would give LaGuerta something to do besides this relationship crap, or at least provide her with a plausible exit from the series (fired for being paranoid and investigating everyone under her). Argh!