I agree that it won't hurt MLB for the most part. For the most part, nobody is really surprised at what went down. They know people do anything to gain a competitive advantage, and may really just be surprised of how extensive this case of sign stealing really is.
However, watching live, I wondered how in the hell Altuve was sitting on an 84mph offspeed pitch against Chapman, when you almost have to be geared up for 100+. I could see a reactionary slap hit or something, but he was timed up perfectly to smash offspeed. Either he guessed right on a 2-1 pitch, or he knew it was coming.
He was perfectly squared up; he either knew what was coming, or it was one of the greatest guesses ever. Knowing what's been alleged now, his actions after the homer are highly suspect: from the preoccupation, after hitting an historic home run, of begging his teammates not to rip off his jersey, to leaving the field to change while his teammates celebrate, to his feeble answer to the question of why he asked his teammates not rip off his jersey ("uh, I don't know... um, I'm shy). MLB may not have found the fire, but there seems to be a lot of smoke.