Possible but not probable. The investigation is related to the CEO and COO and not the company and its overall operation (at least, as far as I've heard). So the bankruptcy process will probably continue without any major interruption.
Well maybe. But I guess that they couldn't find any other way to prevent Apple Pay. After all, neither CVS not Rite-Aid did anything to enable it - it "just worked". So even though PayPass/payWave had been grandfathered (it seems), they felt that they couldn't continue to have Apple Pay work. Or something like that. Whatever it was, it was dumb. Still is.