In both sentences, it is clear that rain stopped play. However, in the first sentence, there is more emphasis on the rain stopping the play. In the second sentence, we can obviously still infer that the rain was the probable cause of the stopping, but this sentence presents things more as a simple sequence of events.
To really get this subtle difference, note that the "had" of the past perfect progressive will often be weakly, or perhaps strongly, stressed (as opposed to unstressed or contracted). This is easier to see if we change the sentence a bit:
- We HAD been playing soccer until YOU came along.
But you can't (with this meaning) say:
- We played (or PLAYED) soccer until YOU came along.
In the first sentence, the until-clause emphasizes the cause of a negative outcome.
To summarize: There may be multiple reasons to prefer one over the other. I have suggested one reason, namely emphasis on the cause of a negative outcome.
Whether the past perfect progressive is the least used tense seems irrelevant. I would imagine the future perfect progressive to be rarer, but I don't have data to hand.