Jean Loring's actions that result in Sue Dibny's and Jack Drake's death are so that the heroes can rush back to their loved ones (Out of fear that the villains may target them), resulting in Ray Palmer rushing back to her. Sound ridiculous given that it's implied that Ray would have no problem getting back together with her. Then again, when you considered the publicity she had gained from the divorce, maybe that's the point. She didn't want to reunite with Ray, she wanted Ray to reunite with her. That way she could get back together with him and save face given that it was he who made the first move and not her.note There are many people who, despite wanting to get back together with their estranged spouse, would rather have them "crawling back." Does it make her reasoning better? No! but it would at least explain a bit.
Along with the rest of the villains who switched bodies with heroes, Professor Zoom gets a mindwipe to forget their identities. This is the Zoom from the future, where the secret identities of 20th century heroes are a matter of public record, who uses this information all the time to attack Barry Allen's loved ones. He would've had no problem telling his friends the secrets of their enemies the whole time without any setup at all. Of course, this simply didn't come up in the original story being retconned.
In fairness, Zoom isn't just evil, he's also a Jerkass that nobody particularly likes.
It also exposes that several heroes could be capably crippled just by the casual reveal of their secret identities, a concept that'd be revisited in Forever Evil. No explanation why Brainiac doesn't begin his invasion with "by the way, Clark Kent's Superman, here's the footage to prove it."
Jean Loring says she didn't mean to kill Sue Dibney, but no explanation is made for why she decided to bring a flamethrower.
Considering she was pretty much insane at that point, it was probably a futile lie to get Ray Palmer to have sympathy for her, which we obviously know did not work.
During Jean's faked assassination, the art shows her being tied up by an unseen assailant's hands, but it's later revealed that she did it to herself... except there's no way she could have contorted herself into the positions seen in the pictures.
She stole another League member's time travel equipment and did it to her past self.
She Hired 2 villains for her scheme, couldn't she just hire someone to make sure that, if Ray, or someone else walked in it'd still look believable, and not like she's trying to manipulate Ray?
They make a big deal about how organized the heroes have become regarding deaths within their circle since Superman's death and have everyone converge on the crime scene and use their specialties to look for clues. Batman, the "World's Greatest Detective" got there before anyone else and yet no one could tell the difference between a chemical fire and a laser. Also, nobody did the most basic piece of investigation and checked the phone records.
They did, but would anyone blink at someone from The Atom's house calling someone at Elongated Man's house? Especially if there's a future baby shower?
Yes, since there needed to be two calls one of which was placed AFTER Sue's death.
Much of the angst in the series was about protecting the loved ones of the heroes, but prior to Jack Drake, the two civilians "attacked" were the wife and ex-wife of heroes whose identities were public knowledge, so there was no evidence that anyone's identity had been exposed.
It's also publicly known that Superman is friendly with the Daily Planet staff, particularly Lois Lane. In the era Meltzer is so enamored with, they publicly dated. So exactly how does a secret identity protect them in any way?
Sue's rape canonically happens in the middle of her career in comicdom, and she shows no signs of emotional or physical trauma outside this series. This series which, by the way, has Zatanna inflicting Laser-Guided Amnesia on villains and Batman for far less pure motives than trying to spare a friend's pain.
Maxwell Lord is seen attending Sue's funeral. Seeing such a good person like Sue die so horribly further dented his already dwindling faith in superheroes, hence his full FaceHeel Turn in Countdown to Infinite Crisis.
The storyline establishes early on that Zatanna and the league had been mindwiping people for a while before they got to Dr. Light. The series also establishes that other villains are as bad or worse than Light — Dr. Moon and Phobia, for instance, are implied to abduct, torture, and murder people as part of their foreplay, whereas Light's rape of Sue was due to a target of convenience. Zatanna removed one rapist from the world, and never attempted to deal with the others.
Bear in mind that Sue was also unique among those targeted during the event in that Sue and Ralph lived very public lives, and Ralph had no secret identity. Sue was raped in the Justice League HQ, but in the long run, she wasn't safer than she was before Light's lobotomy. Any villain targeting the League could go after her.
Light's crippling anxieties afterward led him to murder children just to prove he wasn't afraid of them anymore. In contrast, simply using their security footage and sending Light to trial for his crime would have probably had him locked up the rest of his life instead of getting written off as an expendable asset.
What about Bruce, how much did he subconsciously remember? Tower of Babel? Brother Eye? How much of this was caused because the Leauge's actions. If they hadn't wiped his mind how many of Batman's trust issues, and the consequences of them, wouldn't have been a factor without this incident?