Have them keep manufacturing the 2600 after putting the Super System into production.
I know, I know, it sounds insane, but Atari was actually considering continuing the 2600 as a 'low end' machine, with the Super System as the 'high end' machine...and then someone realized "Uh, what stops our cheap machine from undercutting our brand new machine?".
Terminating production of the 2600 prior to putting the 5200 into production seems elementary; I don't need my MBA to know how insane it would have been to keep cranking out antiquated equipment while trying to launch a new, more advanced (and expensive) system, both of which would be competing against ColecoVision which was a FAR more credible threat than Intellivision ever was. To stave off Coleco, Atari needed to go all in with the Super System, not screwing around with some insane 'high/low' plan.
Since Pac-Man is mentioned, you could also go with the most obvious Pac-related screw up they could have made: Not launch the Super System with Pac-Man as the pack-in. No matter how good the rest of the launch titles were (and Super System had one of the strongest launch rosters of all time), it would have killed the system and Atari both, because a crucial flaw was discovered when testing Pac-Man: The original Super System controller design was going to be an analogue stick. From what I've read, it was a great controller for a lot of really popular games...problem was, as it wasn't self-centering, and that made playing Pac-Man nearly impossible. The minute the developers discovered this, they scrapped the analog design and went with a spring loaded, self-centering, digital stick. Saved the system, IMHO...