Still, that would be a strange storyline, in light of the fact that the Joker and Harley Quinn are supposed to be in jail, and Waller has a connection to them, so he should be aware of the existence of Batman in the first place.
There are definitely ways to go around this limitation of the current storyline though, so we should wait and see what happens once the film has been released. But at this point, seeing “Suicide Squad” as a prequel to “Batman v Superman: Dawn of Justice” is becoming a real possibility and something that could give a hint about the future of the DC Cinematic Universe.
But in any case, it will be an interesting future indeed, as DC have been putting a lot of effort into making their fans happy and ensuring that their universe is being expanded gradually, in interesting ways that keep everyone attached instead of rushing to do as much as possible at the same time.