I think you've misunderstood, the issue isn't that they will throw the cup game or throw the game against us, it's that they may not have an incentive to beat Arsenal when they play in the league this weekend. I'm not saying they will do this, but if they were to let Arsenal win, it would improve Arsenal's chances of finishing 4th, which would give them Europa League in the event that they don't win the final.
Essentially, by letting Arsenal win in the league, they improve their chances of getting European football in the event that they subsequently can't beat Arsenal in the cup. Still, this isn't really a new issue, and it's not as bad as in previous seasons when the cup final was played during the season.
http://www.grandoldteam.com/forum/threads/perverse-incentives-in-europa-qualification.35104/