Having watched a compilation of Loghain's dialogue if you recruit him, I'm a little disturbed to say I actually sort of get where he's coming from in regards to the City Elf situation. It actually makes quite a twisted bit of sense if you look at his logic.
The Elves have no weapons, no training with weapons and live in the most ramshackle and indefensible part of the city, so when the Darkspawn attack, the Elves are screwed. Selling them as slaves meanwhile, will gain the money to rebuild the army, improve defenses and help Loghain end the Blight, an outcome where (nearly) everyone wins. Whereas if the Darkspawn aren't stopped at Ferelden, the Blight will spread, eventually reach Tevinter and the Elves will be screwed anyway.
It's still wrong, utterly deplorable and even Loghain seems to have trouble justifying it to himself in that conversation, but he rationalises it up as simply making a hard choice to sacrifice the few to save the many. When you look at it that way, it doesn't sound that dissimilar to the methods of a certain Ancient Order of Darkspawn Hunters, does it?
Damn... well this makes the Landsmeet trickier?
As much as I want justice for the Wardens, Ostagar and those he sold into slavery, I actually think he'd make a good Grey Warden. Well, for a definition of the word "good" that equates to "as morally questionable and desperate to win as Sophia Dryden". 
And as for Eamon, given that Rowan died two years before Alistair was born, I'm going out on a limb and saying that Eamon told Maric not to raise Alistair. While I agree that he and Maric likely didn't want to diminish Rowan's memory, Loghain is likely right a staunch traditionalist like Eamon wouldn't want someone illegitimate to have any claim to the throne, a claim that would only be reinforced if Maric raised him. Coupled with what we learn in Asunder that a Templar who has taken their vows are usually cut off from any inheritance (although they do have the option to leave the Templars, Evangeline just didn't), it might not have been Isolde who shunted him off into the chantry.