Doesn't say anything that they are the big bads. More likely than not, they're anti-heroes in the avenger rosters since all Joss said was that they create tension within the avengers and/or don't agree with what avengers say/believe. If they were to be the bad guys, they'd would have to bring up magneto and mutant aspect and that's not going to happen. The whole point bringing them in is because they were some of the oldest all time members of the Avengers.
I don't see how they working for Thanos aspect would work.
Disney's Divinity wrote:I've been completely out on
The Avengers and its sequel, but I had no idea X-Men was involved in this.

Need to check the first out now.
No, it's just that those two are the only exceptions in being in marvel cinematic movie universe because those two are big profile Avenger members even long back. Scarlet Witch is like one of the oldest and longest member of the Avengers.
Interestingly enough, Fox ALSO has the rights to Scarlet Witch and Quicksilver too. Just in their case, the Avenger aspect can't be used.