If a judge declines to grant a preliminary injunction requested by the FTC to prevent an acquisition, it does not necessarily mean that the FTC's case is over. A preliminary injunction is a temporary measure intended to maintain the status quo while a case is being litigated. It is granted when a court believes there is a likelihood of success on the merits and that irreparable harm would occur if the injunction is not granted. If a judge declines to grant a preliminary injunction, it means that the court does not find the FTC's arguments convincing enough to warrant an immediate halt to the acquisition. However, the case itself can still proceed, and the FTC can continue its legal efforts to challenge the acquisition through other means.
The judge's decision on a preliminary injunction does not represent a final judgment on the merits of the case. The FTC can still present its evidence, arguments, and pursue further legal avenues to prove its case and seek remedies if it believes the acquisition violates antitrust laws. The judge's ruling on the preliminary injunction is only one aspect of the overall legal process.
It is certainly a type of litmus test for the feelings of the courts prior to the full proceeding that the FTC was going to have to go through anyways. Microsoft was already believed to be willing to close the deal as long as the CMA said yes, seeing as how the FTC was clearly going to drag the case out well beyond the closure date. Not to mention, there was already the general feeling that the courts were going to deny the FTC later. Which has been Khan's crusade this whole time. To show the FTC as toothless and get reforms so that the FTC has similar power in the US to the CMA in the UK, without always having to answer to courts. In processes that are highly political.
As far as how this affects the CMA. It won't either way. The FTC still agrees with the CMA, even if US courts deny them. The difficulty for the FTC to perform its tasks in the US would certainly be highlighted in any attempt to paint the CMA as a loner. In addition to the EC openly sharing the same concerns with the CMA, just being more willing to accept different remedies that the CMA has made clear in the past they find ineffective and very inconvenient. Two important regulatory bodies agree with them. Just that one was willing to deal with behavioral remedies and the other has little of its own power. Not a strong ground to prove irrationality.