Putin probably has Crimea in the bag, at least politically. On March 16 there will be a referendum which will almost certainly vote in favour of union with Russia.
The tricky part for Putin will be removing the Ukrainian forces still in Crimea. It is unlikely Kyiv will accept Russian annexation. So far, the Ukrainian soldiers under siege have shown admirable restraint and have not responded with violence to the provocations by the militias and "self-defence forces". Ukraine has learned the lesson of the 2008 South Ossetia War when Georgia's armed forces gave Putin the excuse to take military action and drive them out of the region.
Putin will gradually build up the Russian military presence in Crimea in the hope the Ukrainians will back down in the face of overwhelming odds (last time I looked there were already supposed to be 20,000 Russian soldiers in the peninsula). Last night, a small band of Russian troops tested Ukrainian resolve and attempted to take over a base. They failed, but we can probably expect more such experiments over the coming days (or, more likely, nights).
If the Ukrainians still hold their bases after the annexation referendum passes, Putin can declare they are now the real "occupying forces". He may allow them an honourable way out by letting them leave with their weapons. Or he may push for unconditional surrender. It depends on how much he wants to humiliate Kyiv for its insubordination to the Great Russian World Order.
However, the real wild card - and the biggest danger - in the Crimea at the moment is not the Ukrainian and Russian regular soldiers but the pro-Russian militias. They are there to give the Crimean coup the appearance of a popular uprising. They are also useful for beating up journalists and pro-Ukrainian protesters as well as threatening potential outside monitors such as the UN and the OSCE. They will ensure that the referendum avoids detailed international scrutiny.
Some of the militiamen are locals, but many have obviously been brought in from Russia and elsewhere. There are supposed to be Russian Cossacks and Serbian "Chetniks" present, for example. I remember reading in Thomas de Waal's book The Caucasus: An Introduction, which covers the wars in Abkhazia, South Ossetia and Nagorno-Karabakh, that the worst atrocities were carried out by such "tourist" irregulars. Local people were at least aware that they would have to live with their neighbours after the conflict was over. The danger came from outside volunteers bussed in to join the fighting - young men pumped up with nationalist sentiment, with little training or discipline and no sense of responsibility. Basically, football hooligans with Kalashnikovs. For example, in Nagorno-Karabakh the Khojali Massacre of 1992 was blamed on the undisciplined behaviour of the "Arabo" and "Aramo" Armenian paramilitary units. It's also worth investigating the biography of Shamil Basayev, who began his guerrilla career as part of the Russian-backed "Abkhazia Brigade" and ended it as Moscow's Number One Chechen terrorist leader.
Putin may think he has these militiamen under the thumb of the regular - if badly disguised - Russian army. But they have a way of making their own rules and a brutal talent for aggravating ethnic conflict. So far, there has been thuggery but no deaths in Crimea. This could change with the click of a trigger.