It's an odd/interesting/surprising directing choice, but I love it.
The funny thing is people hear odd pairs involving movies (Heath Ledger cast as Joker) and automatically close their mind about it. We all saw how the Joker was with Ledger. I think Mendes could make this amazing.
With Peter Morgan writing the script, it should have a good story too.
Ledger wasn't directing The Dark Knight though. If Sam Mendes was playing James Bond then your defense would make more sense.