The stop without probable cause is the only problem, assuming laws regulating drugs and traffic are legitimate.
How should the discovery of an active warrant and drugs be handled after an illegitimate stop? Should the officer be disciplined, or be charged with abduction? Should the drugs be returned to the arrestee, or should the warrant be reactivated upon his release so that he can be legitimately found? I would hope the justices asked themselves some of those questions in reaching the decision, instead of just blindly siding with a government.
If checkpoints are legal, it's hard to put up much of an argument against a stop that is at all related to an actual investigation.