I don't think When Flanders Failed is meanspirited at all. Homer is no worse than in Dead Putting Society, and it's just another case of jealousy. Homer had no idea Flanders depended so much on his store he would be rendered homeless if it failed. As soon as he realizes the consequences of his actions, he feels a stone going down in his throat. It's not like Co-Dependents' Day where Homer intentionally did something which he KNEW could have ruined Marge's life, drunk or not. He only wanted Flanders to have something less to brag about, not live on the streets.
Another difference between those episodes is that Homer actually does something to redeem himself. While in Co-Dependents' Day he just waited for Marge to crawl back to him (not to mention he did something more unforgivable), he felt so ashamed that he did something which not only put Flanders back in business, but resulted in him making more money than ever. The ending is not Brady Bunch esque (whatever the heck that means), it's a heartwarming ending which was earned since we rooted for Flanders and feel thankful that Homer did something actually nice for his neighbor.
I also disagree about the lack of humor. I laughed so hard at this episode, Homer's stubborn naivety made for some very funny one-liners, and the scene where he chokes on a hamburger is one of the greatest visual gags ever.
When Flanders Failed is a top 50 episode, not bottom 50.