But in fact, he says exactly the opposite in the decision. Read this paragraph, from page 49:

The Speaker has also suggested that such an explicit caution about Christian references "would be the first known religious viewpoint discrimination in connection with the Indiana House invocation." ... The criticism is misguided. The decisive point of constitutional law is that a practice of sectarian prayer favouring any particular religion violates the establishment clause.

From the evidence here, it is clear that the letters asking invited clerics to "strive for an ecumenical prayer" have not been sufficient to prevent many Christian speakers from using the prayer opportunity to advance and even to proselytise Christianity. The same strictures will apply to sectarian Jewish or Muslim prayers, for example.