Late answer, I didn't downvote this though.
Anyhow, both formulations of entropy - the thermodynamical one with the integral and the statistical physics one with multiplicity - are equivalent. At least the latter already contains statistics because of the combinatorial part.
And then there is one formulation of the 2nd law which states that on statistical average the entropy rises. So it doesn't break the law if it falls down. Given that this quantum computer doesn't involve many objects, the number of combinations isn't that high. But it's nice to observe Entropy falling! (And there are other situations in which this can happen anyway.)