Quite rightly, there’s increasing attention being paid to the prospects of minority communities in Syria during, but especially after, the civil war. From Stephen Starr’s valuable reflection on the ambiguities of the conflict:
Today, the regime is openly espousing sectarianism (for example, it has supplied weapons to Alawites living in the Mezzah 86 area of Damascus), but so too are Sunni civilians who back the revolt. Alawite civilians in Syria are being murdered for no other reason than their religion … One Syrian working in the international press told me that Sunnis and Alawites can no longer live together, that some Alawites should be pushed back to the mountains of western Syria.
As one survivor of the Houla massacre told Channel 4’s Alex Thompson:
He says to us: “They have slaughtered us, they have killed us. When this is all over we will be victorious. And we will go there. And we will find them out and we will slaughter them and we will kill them. We will kill their men, women and children as they killed our men, women and children.”
One thing to remember is that this type of retribution is typical of such bitter conflicts. You will recall the ethnic cleansing in Iraq, but this is prevalent even in the aftermath of conflicts other than civil war, and even from groups that we, near-universally, consider as righteous and noble.  Tony Judt, in his brilliant history of postwar Europe:
In France some 10,000 people were killed in ‘extrajudicial’ proceedings, many of them by independent bands of armed resistance groups, notably the Milices Patriotiques, who rounded up suspected collaborators, seized their property and in many cases shot them out of hand.
About a third of those summarily executed in this way were dispatched before the Normandy landings of June 6th 1944, and most of the others fell victim during the next four months of fighting on French soil … no-one was surprised at the reprisals – in the words of one elderly former French prime minister, Edouard Herriot, ‘France will need first to pass through a blood bath before republicans can again take up the reins of power’.
The same sentiment was felt in Italy, where reprisals and unofficial retribution, especially in the Emilia-Romagna and Lombardy regions, resulted in death tolls approaching 15,000 in the course of the last months of the war – and continued, sporadically, for at least [!!] three more years.
In Poland, the main target of popular vengeance was frequently Jews—150 Jews were killed in liberated Poland in the first four months of 1945. By April 1946 the figure was nearly 1,200 … the worst pogrom occurred in Kielce (Poland), on July 4th 1946, where 42 Jews were murdered and many more injured following a rumour of the abduction and ritual murder of a local child. (pp.42-43)
Europe did pretty well at stemming the tide:
[N]owhere did the unregulated settling of accounts last very long. It was not in the interest of fragile new governments, far from universally accepted and often distinctly makeshift, to allow armed bands to roam the countryside arresting, torturing and killing at will. The first task of the new authorities was to assert a monopoly of force, legitimacy and the institutions of justice … This transition took place as soon as the new powers felt strong enough to disarm the erstwhile partisans, impose the authority of their own police and damp down popular demands for harsh penalties.
The disarming of the resisters proved surprisingly uncontentious in western and central Europe at least. A blind eye was turned to murders and other crimes already committed in the frenzied liberation months: the provisional government of Belgium issued an amnesty for all offences committed by and in the name of the Resistance for a period of 41 days following the official date of the country’s liberation.
All in all [in France] the épuration (purge), as it was known, touched some 350,000 persons, most of whose lives and careers were not dramatically affected. No-one was punished for what we should now describe as crimes against humanity. Responsibility for these, like other war crimes, was imputed to the Germans alone. (p.44)
 There’s a useful edited volume on this: The Politics of Retribution in Europe:World War II and Its Aftermath, edited by István Deák, Jan T. Gross, and Tony Judt
Update: David Gardner has an optimistic view of rebel discipline in his FT column this morning:
When [the Assads] do fall, there is natural concern about what will replace them – especially since the Wahhabi Saudis and Qataris are directing their support towards the Islamist Muslim Brotherhood. Yet despite the regime’s slaughter of (mostly Sunni) civilians, and a few attested rebel atrocities, there have been no mass reprisals against the minorities. This suggests discipline and deliberation by opposition forces on the ground: the regional military councils and the local co-ordinating committees of activists driving the civic uprising. As in Libya, an international alliance against the Assads may have something to work with.