They can't be used safely, that's the point. The smoke is either unpleasant and dangerous to breathe, or the marine flares are an actual fire hazard (they're designed to burn at very high temperatures).
The way to make it go away is the same as anything else unacceptable or dangerous, educate, enforce, and if necessary prosecute.
Just saying we've got to accept it because it's here makes no sense; plenty of other things that used to be broadly tolerated in the grounds aren't now (e.g. racism, drinking in the stands, fighting, and even bottle tops!), why should flares be any different?