He should be considered innocent by the courts - and he was (innocent of the murder for hire charges, I mean). In the public we aren't obligated to follow the same standards of evidence as the courts. I think he almost certainly did pay to have those people killed, and that can shape my opinion of him.
That's perfectly reasonable - but I don't think it should really have a bearing on whether he should be pardoned. That is not exactly a matter of the courts (by definition), but I think as an official public act it should be subject to the presumption of innocence as well.