Should that count in favor of or against the church that excommunicated him (in this case, Presbyterianism)?

Of course in favor.

Assuming conservation of evidence, if there exists an action that would count against them (such as declaring him a saint), there must also exist an action that would count in favor of them. So what exactly were they supposed to do -- burn him at a stake?

EDIT: Oops, now I see that the question can refer to the whole "former membership + excommunication" package, not just the "excommunication" part. Still, unless other churches had excommunicated such people (before the murder, or at least after), the fact that this one did is an evidence in favor or hypothesis that they disagree with such acts.