I can see Eisenberg's Lex as the target that Amanda Waller orders a hit on, and she hires the Suicide Squad as a team of assassins to take him out... BUT, Eisenberg isn't really in the movie for more than 5 minutes, or more than a glorified cameo where Zack Snyder literally shoots his scenes separately in one day on the set of BvS. He's depicted through spy photos and audio recordings, and files, etc.
I'll be honest, I'd love that. It turns into a heist film where the Squad has to figure out how to break into LexCorp, fight the armed bodyguards, bypass and hack through security systems, etc. And maybe we find out that one of the Squad members like Deadshot is actually double-crossing the team and has been working for Lex the whole time.
Combine that with Harley Quinn's antics, and you basically have Ocean's Eleven From Hell. That has my money instantly. It's really The Anti-Justice League, and could make for very entertaining counter-programming.