Assessing Turkey's options against the PKK's attempts to establish an autonomous zone inside Syria is not an easy task for two reasons.
First, unfortunately, Turkish authorities like to make overemphasized statements and use big words during a crisis and subsequently forget them when the crisis has calmed down. When a Turkish jet was downed by Syrians, the prime minister and foreign minister used big words and made large promises about what Turkey would do to Syria. The prime minister's words against the Syrian regime were so strong that the international community thought Turkey was going to wage a war. In the end nothing happened. In recent years there were a number of issues that the Turkish authorities were so vocal about but did nothing about any of them. All in all, comparing their words and their actions, Turkish politicians do not practice what they preach. Therefore, we cannot take the Turkish authorities' promises seriously while trying to make any assessments.
Second, we don't have much information about the PKK's capabilities inside Syria to make an assessment. Several intelligence reports have indicated that the PKK deployed some of its units inside Syria but we don't know their size and capabilities. Furthermore, the PKK is an organization that is trained to fight in the mountains. However, what is emerging inside Syria is taking place in major city centers. Therefore, for the PKK as well, Syria is a strange territory to defend even if Turkey intervenes militarily.
Further, the very own future of Syria is unknown. We don't know how long this crisis will last and we don't know how other Syrian groups would react against the PKK's autonomous zone in their country.
Realistically speaking, Turkey does not have many options against the PKK's autonomous region inside Syria. One could even argue that Turkey has no option to intervene inside Syria.
Instead, Turkey should try to use diplomatic pressure to “balance” out the emerging PKK zone inside Syria. I use the term “balance” because Turkey has no option to remove the PKK from Syria. It is too late for Turkey. Instead Turkey should use other apparatuses to “balance” out the PKK's existence.
Diplomatically, Turkey has two practical options on its side. The first is using Massoud Barzani's influence over Kurds to try and “balance” out the PKK's existence. In addition, Turkey should stir up Arab nationalism and unrest against the PKK to “balance” out the PKK's activities.
In fact, Davutoğlu is visiting Barzani as a first step to “balance” the PKK-related developments inside Syria. However, Barzani's influence in Syria is limited. The PYD sat down with Barzani to negotiate over the future of Kurds under their territory not because Barzani had influence over the Kurdish groups there but because the PYD, or the PKK, needs Barzani to legitimize its existence in Syria. Thus, the PKK sat down with Barzani in order to earn some legitimacy. Turkey, however, visits Barzani to delegitimize the PKK's existence inside Syria.
The second option is Arab nationalism. The Free Syrian Army and Syrian National Congress have especially shown their dissatisfaction with the developments inside Syria. However, their ability to stop the developments is very limited, or almost none. Furthermore, while the Free Syrian Army is busy fighting against the Assad regime, it cannot devote some of its militants to stop the PKK from establishing its bases in Kurdish territories.
In addition, the PKK's argument for establishing such authority in Kurdish regions is to keep Arabs away from intervening in Kurdish affairs. The PKK has declared several times that Turkey is supporting Sunni Arab groups to stop the PKK. Thus, the PKK has not only prepared itself against possible Arab pressure but it has prepared the Kurdish population to distance itself from Sunni Arabs as well so that they can hold on to the gains that they earned. So the Arab card against the PKK would not work either.
All in all, Turkey does not have many options to stop, or slow, the developments that are helping the PKK establish democratic autonomy inside Syria. One could even argue that it is a lost cause for Turkey.