The main problems with boundary layer drag control methods have been practical. IIRC Airbus tried huge swathes of some kind of special 3M film on a A340(?) but the big problem was maintenance. Either the damn film peels off (and flaps around in the breeze) or you have all kinds of issues with baggage doors and access hatches and such. The film used was more rippled or grooved than dimpled, I think, but it was a vaguely similar mechanism at work.
And yes, applying something like that might be problematic to the wing; though I'd be far more concerned at attempts to maintain laminar flow characteristics than deliberately inducing turbulent flow; the former would probably break down far more catastrophically.