I think what we see in Iraq is a replay of Iranian post revolution politics.
In my opinion, Khomeni in 1978, just as Sistani in 2005 wanted an Islamic country run by politicians with clergies in the background. May be Khomeni to lesser degree than Sistani, but if you go back to history of Iran right after the revolution (1979) you see similar patterns. In the original Iranian constitution the President of Iran was head of the armed forces and most of the government officials were non clergies. But facing incompetence of the president (Bani Sadr) in facing Saddam's invasion, and the Kurdish rebellion Khomeni had two choices, either to sit on the side line and essentially see the country go up in flames, or take center stage. He choose the later, the president was ousted, the constitution was modified and made himself (with title of “the leader”) to be head of armed forces and the final say on all matters.
I see Sistani being on the same crossroad as Khomeni in 1979. He can sit on the side line and essentially make himself irrelevant or at some point he (or someone like himself) has to become “The Leader”. It is a difficult choice, and has its own set of problems. With clergies in power, it means they are responsible for daily affairs of the population, Sistani wants to avoid that but he may not have a choice. There may not be any other choices if there is to be any future for Iraq. Specially since 3 months after the election, there is no government in place, and US ambassador seems to be eager to micro manage the process for its own goals.
President Bush said: "..And if you believe that, then you have faith in people demanding freedom, if given a chance". To which I have to say... What I see in US policies on Iraq is that there doesn't seems to be any "faith" in Iraqis, and they are not "given the chance" to govern themselves.
We are three years into the occupation, something like 2 trillion dollars have been spend in Iraq (most likely Iraq now owes more to the rest of the world than the end of Saddam regime) and lives of Iraqis is getting worst every day. Three years into Iranian revolution, Iran was fighting Saddam and was able to push back Saddam's army and turn the tied of the war. With the current political leadership in Iraq, and the American/British occupation there is no hope for it dealing with the insurgency and bringing any sense of normalcy to lives to lives of Iraqis.
The Iranian model may not be perfect, but facing a deteriorating situation in Iraq, I would expect the religious leadership to step in and play more assertive role. Thanks to Geroge W's policies, secular voices within the middle east may well be at their weakest point in history.