Why did Link get imprisoned in the mirror? He didn't have the COURAGE to face Ganon by himself! Because Harkinian took the TRIFORCE OF COURAGE.
The TRIFORCE OF WISDOM said the King would safely return. Nothing was said about "when" or "with whom".
Eating an Octorok wouldn't really be that bad. If you think of it, Octoroks are just Hyrule version of octopuses, and octopus is a delicacy in some countries.
Only Link can defeat Ganon... Except Gwonam was talking about the Island of Koridai. It wasn't said that Zelda couldn't go defeat him in Tolemac or in Gamelon.
King Harkinian sentencing the traitorous Duke Onkled to "scrubbing all the floors in Hyrule" seems like Cool and Unusual Punishment at best...until you consider that Hyrule is also home to many dungeons full of deadly creatures, and Onkled would have to scrub the floors of those dungeons. In other words, it's a death sentence in disguise!
Or he could have just meant the homes of all the citizens in Hyrule, which is still embarrassing and grueling for someone who is a duke.
Why does the General Store guy act so suspicious? When you don't have enough rubies, he says, "You'll have to wipe out a few more Goriyas to get that." Considering that in Faces of Evil every Goriya Was Once a Man, this may mean that the shopkeeper is aware of it and still encourages Zelda to kill the transformed citizens for their money.
Those metallic, robot-like soldiers with the spears that appear in several levels? One cutscene shows that they're ordinary (possibly innocent) people being transformed into enemies, likely against their will, and brainwashed into killing Link. Or perhaps they're mentally aware of what they're being forced to do, but helpless to stop themselves. Keep in mind, these are just run-of-the-mill baddies that as Link and Zelda you're killing off on a regular basis.