Yes, there was certain disturbing effect of the tiny and lonely Nanoarchaeum genome, yet the Halobacteria is a very specific clade, forming a tightly connected group and moving around as a whole, mainly due to the biased acidity of their constituent amino acids. We anticipate that the relative placement of Halobacteria with respect to other groups may stabilize when more genomes are used to construct a tree.
Even if defined in the future, it must be lineage-dependent.