The next new episode of MLP is coming not this but next saturday. Discord returns and Fluttershy wants to give him a second chance. Because of the rule about staying up to date with the show if Discord becomes a good guy we cant use him as a villian. Any ideas?

Use him as a villain anyway. We could say that he either lied about becoming nice, or have Chaos re-corrupt him.

My story is slow in a way, so I'll wait and see how the next episode is going to turn out. As a matter of fact, I'm still thinking whether or not to have Discord be one of the antagonists for my story.

I actually haven't started mine yet (I should probably get on that), and I never thought of using Discord as a villain. But we could just stay canon with the show until the end of season two. So our story could be canon with the show for the first two seasons and season three premier seeing as though that was a pretty big deal.

1. There is no given timeline so perhapse this story simply takes place before said episode.
2. I would however support the wait and see aproach

Hmmm this should be interesting to see how discord will turn out. May affect some of your stories.