I'm probably as resistant to pure majoritarian democracy as anyone you're going to find, but the answer is:
It is totally and completely legitimate to use reconciliation as a vehicle for passing health care reform. Conservative claims that reconciliation shouldn't be used should be given about as much weight as complaints about White House czars: in other words, none at all. There's nothing in the law or the precedents of reconciliation that would even hint that it shouldn't be used for something like this. It is not, as the NYT claims Republicans will cry, "parliamentary trickery." It is part of the standard rules and procedures of Congress. Objecting to the use of reconciliation is basically similar to stalling a vote all day and then complaining that the vote was taken in the dead of night; it might con a few especially dimwitted rubes, but it's not a serious argument about fairness or democracy.
Of course, that's a totally separate question from questions about the technical difficulties of using reconciliation. And there's a real political problem: if reconciliation was used for the main bill, it's not at all clear that the Democrats could get 50 votes, because marginal Democrats don't want to vote for something that only has the support of liberals. Those were good reasons for the Dems not to use reconciliation as the primary method of passing health care reform. But on grounds of fairness or democracy? I've been unkind to Kent Conrad lately, but no one is going to top this:
As for the Republican criticisms of the tactic, Conrad said that "they are going to say that, whatever."