i never liked her E, but i dont think it looks stupid in ms paint or in the game. it made sense when she was an angel. if you were to tell me that kayle glows a fiery red and gains a halo when she uses her E i would be like... oh she's an angel? you wouldnt have to say anything else. giving morgana chains and a broken halo doesnt do that same thing. giving her chains makes me think she's a ghost or an escaped prisoner. giving her a broken disk above her head makes me think she's got a bug going on with her since broken disks dont signify fallen angels. horns and damaged wings do. so that's what i mean when i say that the image of morgana covered in chains with a disk over her head doesnt make sense. especially if we're trying to make their kits remotely similar to what they are currently.
not having a halo in the first place when they're not angles or demons is step 1 to making a decent rework. if there are no angels or demons it's better to not make them seem like angels or demons.
step two is to remove their elongated ears. the simple fact that morgana looks like an elf and that her ears do not even remotely resemble her character portrait is annoying to say the least. we dont want to mistake her for whatever race janna is or for a humanoid yordle hybrid or a vestayan.
for that same reason (not mistsaking her as a vastayan) we should remove OR change her wings. if you look at all of the current champions that are darkin they have a sort of melted flesh with rocky bone look to them. almost dragonic in a sense. i dont personally think her wings would be appealing if they were to become like aatroxes
aatrox for example has wings, but they dont look anything at all like normal wings. they're bent and extremely veiny. they appear to be made of rock and magma rather than bone and flesh with a red and greyish color pallete.
http://stickskills.com/wp-content/uploads/2013/05/league-of-legends-aatrox-model.png
varus looks very similar to his old model with a few changes to hues and such. this was likely for aesthetic purposes so that the fans would still enjoy varus's look. what varus shows us is that darkin can cause a blackish/purple color as well as the red/grey color tint. so morgana could still have her blackish/purple color except it would need to be changed a bit and made more crystalline. likely more so towards her upper body if she continues to wear her dress since the crystallization replaces flesh not clothing. you can see that with rhaast.
http://orig15.deviantart.net/867c/f/2012/161/f/d/fd1b6b424c0e037a25ddd82c6f8eead3-d52zeal.jpg
kayn and rhaast were designed specifically to be the darkin guide to follow. so Rhaast shows us what a darkin looks like and kayn shows us what happens when a darkin has been conquered as well as what it might look like when they're inbetween those forms. once again with rhaast we see those dragonic/demonic looking elements. the biggest thing to note about shadow form kayn is that shadow form kayn takes many many years of kayn's life to accomplish and is only a hypothetical. hence the long black hair as opposed to his initial shortened ponytail that's wrapped. it also signifies that he's awakened. the one major thing to note though is that rhaast is creeping in through the hand that kayn carries his weapon with. if kayle has conquered a darkin she would no longer look like a darkin at all. in fact the shadow kayn outfit has no traces of darkin involved with it. instead the weapon has become more powerful and has reverted to it's normal state.
https://3.bp.blogspot.com/-c4J7MDIrLr0/WVMtKp1rCcI/AAAAAAABEQA/5omxTG3PzCoRsrYopwTp1Foyf4txnXyNQCLcBGAs/s1600/kayn3.jpg
if we think about kayles sword she has several of those blue colored gems in her sword and one very big one at both the hilt and the tip of her sword. this would be a prime place for her blue "eye" of her conquered darkin. but because she's conquered it the lack of darkin properties in her sword and appearance should be noted. if morgana has fallen victim to the darkin then her form would be more akin to rhaast and no longer human. so she couldnt be completely conquered. she'd have to be in a state of limbo like varus. Morganas current appearance is that of a woman with fairly normal lower and mid section that is very pale/white with elongated fingers, elongated ears, and unique eyes. she currently has damaged eagle wings that are purple. since she carries no weapon and the majority of her changes are on her mid to upper body i think it would make sense to either imbue her crown with a darkin gem or give her a pendant that is imbued with a darkin gem. this could become the "eye". I want to point out though that there doesnt need to be an eye. varus has no eye on his bow.
halos and horns are not present in shadow kayn or varus nor are their ears elongated. if morganas ears are to stay elongated then the crown would make the most sense as it would explain her ears.
one solution to your desire to grant morgana chains is that you COULD put some anklets on her legs, some wristcuffs on her hands and give her a broken chain coming from each that signifies she IS an escaped prisoner. that she was imprisoned due to the darkin having majority control over her mind, but since she's kayles sister she was imprisoned instead of being killed. or perhaps they were trying to cure her of the darkin.
instead of a clean and pretty dress she could get a torn dress that exposes her feet being transformed into the crystaline like darkin flesh.
her wings would need to go. or they could stay as long as they're changed from an eagle's appearance to a more crystalline and rocky form - which i dont think would be all that appealing.