Another source quoted Stupak as saying that he had offered Pelosi 7 or 8 different ideas to address the abortion funding objections and she didn't want to hear them. I think it's safe to say that he and his coalition would probably vote for the Senate bill if it did not allow for federal funding of abortions.
I think he's using his leverage to get enough people in the House and the Senate to consider whether health care reform is important enough to them that it would be worth dropping the abortion funding.
I think Stupak and his ilk want Pelosi and Reid to try to cobble together enough votes with the abortion funding dropped. If it's that or nothing, Pelosi and Reid might be able to get it done. But it would take more time and time is something they do not have.
Stupak will in the end vote for the health care bill I think because he is a worthess POS with no conviction beyond party loyalty. The ball is in his court.