Slate‘s Timothy Noah offers a guess as to why Rep. Stupak held out for a meaningless executive order:
As of yesterday, the White House was willing to promise Stupak an open-ended ban on abortion funding in the exchanges. But today, either because of blowback from pro-choicers in Congress or because Stupak lost some leverage as the health reform bill acquired more votes, it was not. So a basically meaningless executive order was issued to help Stupak save face.
See his whole post for more background.