If you scan the JVO questions related to Israel you will find several variations on this theme. The general question regarding the appropriate boundaries in discussing Israel – as a private individual or as a community leader, as one concerned about aspects of Israel's policies or as one disturbed by the public pronouncements of others – can be complicated. The questions and responses found elsewhere on the JVO site will be instructive.
The NYTimes article you refer to can be found at http://www.nytimes.com/2012/10/21/us/church-appeal-on-israel-angers-jewish-groups.html ). The statement by the 15 church leaders is particularly disturbing because it seems, according to news reports, to have also broken a long-standing conversation that existed between these leaders and various national Jewish leaders. I gather, without any direct knowledge, that there was a sense of betrayal felt by some Jewish leaders when this statement appeared.
Your question suggests that you are not a community leader who bears a particular obligation to represent the Jewish point-of-view to the general public, and I will frame my response on that assumption.
I believe there are a few avenues of action open to any concerned Jew.
Education begins at home – I understand the anger that one might feel about a statement such as this, but effective responses are based on knowledge more than emotion. So the most basic step is to be clear on your own grasp of the relevant facts. Continued reading, conversation and study on the situation of Israel and her neighbors is essential if one wishes to be heard in the public arena.
Community action – There are any number of agencies who work to present Israel's case to the American public. Your active support for any of these organizations that match your concerns and outlook allows you to have a voice in the public debate.
Political support for Israel – It is certainly possible and responsible to counter this appeal to Congress with one's own appeal. Calling your own congressional representative and signing on to any petitions (if they exist) supporting continued aid to Israel and/or a repudiation of this letter is an effective way to participate in this debate.
Dialogue – We have seen evidence in similar instances that the leaders may not reflect the beliefs of their followers. There were many local contacts made between the Jewish community and the Presbyterian Church USA regarding their move toward divestment, and the effect of local dialogue was decisive in the narrow vote to defeat the resolution. The continued honest dialogue between individuals can have a dramatic effect.
Confrontation – There are times when confrontation is crucial. The Torah describes a process for rebuke when one steps over a line of misconduct. The rules are complex, because you bear a similar responsibility not to shame the offender. Nonetheless it can be helpful to speak directly to the offender and to let them know in what ways their concerns have crossed the line. Would such an approach, change the mind of these leaders? Perhaps not in the short term, but it may serve to open direct or indirect lines of communication for the longer term. It also puts the disagreement into the public eye, encouraging others to take a stand.