If you'd be a little bit more humble here. A statement you could make to Tom would be:

Yes, the church has changed over the years. While I believe that the Church was established by Christ, it has been run and codified by man for 2,000 years. For example with amendment 10-A, the church has been researching and debating this issue for decades. After much discernment and prayer (hopefully there was much prayer), the church decided that its fundamental understanding of the position and place of practicing gay clergy has been made more clear. The Church believes, based on Biblical Scholarship, discernment, and the collective understanding and belief of its members, that practicing gay people can be called to ministry by God. We feel that it is important to seriously study, pray, and seek counsel when we find our faith and understanding of the truth to come up against seeming contradictions or incongruities. Faith in God would be lessened if we were unable or unwilling to study our beliefs and adjust them when it becomes clear, Biblically and Spiritually, that we have misconceived aspects of God's truth.

Most people are skeptical about churches and faith because they see it as this single monolithic belief and management structure that hasn't at all changed in any way in over 2000 years. As far as I can tell, the Presbyterian church believes that it has a better understanding of God and who he can call to his ministry, not that the truth has somehow changed.

That won't change that some people will disagree with you for a variety of different reasons, but it isn't a defensive stance that serves no purpose to your Church or mission.