Firstly, to answer your questions, yeah, you do bring up a valid point. Testing the morals of the main characters is the best (and easiest) way to create conflict & foster growth in said characters. Though as many brony reviewers have undoubtedly brought up, rely on this too much & you make them look weak & wishy-washy.
Generosity I have a hard time placing, as I find it hard to separate from loyalty & kindness. Judging by the examples given in the show however, it seems to carry a connotation of self-sacrifice. Something Nightmare Moon clearly balked at when she refused to share time with her sister & enforced her will upon the populace at large. Agree whole-heartedly with you on that point!
Loyalty, as I see it, is somewhat like honor. Wanting for the greater good & thinking of others. The opposite of this would be taking from others & considering yourself the greater good. When Tirek showed up broken & clearly hating the world it became apparent that he viewed himself as the only being worthy of wielding any power at all. I cast my vote for Tirek as the Element of Avarice!
I agree to deception opposing honesty. The entire basis to Chrysalis's species is looking like other ponies, about as far from being true to yourself as can be! Maybe if Chryssy was honest & walked up to the front gates with a "Hey, my hive is going hungry, can we borrow a cup of love? We promise it'll likely not hurt much." we could've avoided the whole hullabaloo, but hey, wouldn't have had an episode then!
Kindness is a bit much like generosity. Willing to give & not expecting a reward, but more of a focus on trusting in others. Sombra was cruel, yes, there's no denying that, but that was when he was alive. The crystal ponies knew very well what he was capable of and when he came back as a...uh, smoke monster there was no way of stopping him. Sombra used those around him & only saw them as objects to take from. Sombra wasn't just an example of it, but an embodiment of fear. Going so far as to have a magical doorway to paralyze you with your worst fear; odd how he'd keep that under his throne where only he could get to it...
As for the opposite of magic, well...I sort of see magic as a tool. Sure magic can be used for good or for ill, but it's meant to help. You could use that hammer to build homes for the homeless...or bash someone's skull in with. But the point is to HELP.
When Starlight Glimmer showed up in her episode, it was her town, her way of thinking. There was one side to be on, and that side was hers. We still see this a bit in her personality, as she's the pony more reluctant to try new experiences and the first to offer criticism or get in the way when things aren't going a way she's comfortable with. As the opposite of magic & the Element of (for lack of a better word) Order, my vote is for Starlight Glimmer!
*cough* Mayadere pony is best pony *cough*
And lastly, Laughter! Way I see it, laughter is sort of its own opposite. If we use Pinkie Pie as an example, the show means laughter as a means to spread happiness, yet still being responsible to know that sometimes, you don't have to be at 100% full-bore ecstatic joy to be happy. The opposite isn't so much as being unhappy, but happy for the wrong reasons. Laughing at the EXPENSE of others, rather then with them. That is what we get in Discord. When he separated the girls in his debut episode, he did so because they would have ruined his plans, and his fun. As we saw in Starlight's parade of alternate timelines, if Discord had his way, everypony would be his puppets & playthings. I vote Discord as the Element of Manipulation!