1. Deposition phase... the case is already underway.
Which is a bit different than already at trial.
2. To high profile of a case to simply "drop the charges" without a d@mn good explanation. The mere look if impropriety on the administrations part would be enough to get a ton of negative attention.
Which is a bit different than impeachment for judicial interference.
3. See point 2., they would have had a lot of explaining to do.
Or the charges could have never been brought at all.
Or they could have said that they have no direct evidence of Apple deliberately fostering collusion among the publishers and claimed that the existing settlements with the publishers will resolve any negative market impact. (But then they would have to explain why they forced Apple to modify the private contracts that they negotiated with the publishers in good faith without any due process.
)