Stupak did right but has to keep it a secret (I think).

If the federal courts behave as they have in the past (see the very solid USCCB analysis of prior cases), the new healthcare law, despite the slightly pro-life wording of the executive order, will dramatically promote abortion. Funding for elective abortion will be included in healthcare wherever it is not specifically excluded. So pro-life Representative Lipinski  (D-IL) was prudent in voting against the bill and in stating: “I do not believe the last-minute effort to address these [pro-life] concerns through an Executive Order is sufficient because there is every indication that federal courts would strike down this order, and the order could be repealed at any time in the future."

But it is also true that the Administration's interpretation of the new law, through Obama’s EO, could positively affect the federal courts (especially the five justices on the Supreme Court who are more open-minded on abortion); those justices might ultimately say the EO provides a reasonable way to understand the law. Abortion will then (to some degree, though not perfectly) be excluded from healthcare funding where it is not specifically included. So Stupak was prudent in voting for the bill if that was the only way to get an ameliorative EO onto a bill that would have passed anyway.

But, it will be said, “By counting votes we can see that the Senate bill clearly could not have passed in the House without the help of Stupak and his group. So he could have altogether stopped an expansion of abortion funding, but settled (at best) for just limiting that expansion.”

Such a criticism may, however, be misguided. According to information I believe trustworthy, Pelosi had told Stupak that she  had the votes to pass the Senate bill without any pro-life support, but she would have had to lean on a number of new Democratic House members from very conservative districts where voting for the healthcare bill would have greatly threatened their reelection in November. That is, the leverage Stupak had was not "If I and my group don't vote for this, it's dead." His leverage may well have been only "If I and my group don't vote for this, you'll have to call in votes from marginal districts and thus make it harder for the Democrats to keep their majority in the next election." In the latter context, getting a moderately pro-life spin on the bill via the EO was an achievement.  It was arguably a deal worth making.

If I am right about the politics, then Stupak et al. voting against the bill (though perhaps making them look heroic, like General Custer) would have accomplished nothing legally and would have made pro-life Democrats look irrelevant rather than (as they do now) a group with some clout, one that must be dealt with.

But Stupak cannot come out and give this defense of himself in public, I think, because it would undercut the voter support for those marginal Democrats that Pelosi wanted to secure by her deal with his group, and would thus make her less likely to strike a deal with him again. Thus, perhaps, the poor guy has to put up with being accused again and again of having brought a federal abortion funding mandate to America when he knows that’s not true.