The disaster of Manzikert lied not with the battle in of itself but in the events that followed. The direct consequence of the battle was that for the first time since Valerian that a Roman/Byzantine emperor had been captured by an enemy power.

Now, it had not been Alp Alsan's intention to become involved in an extended war with Byzantium given that the Seljuk Turks' principal enemy were the Shia Fatimids of Egypt (The Turks had in the recent past become Sunnii and fundamentally opposed to the Shia). Thus, Alp released Romanos IV on the conditions that he would pay the Seljuks 1.5 million nomistia (gold coins) and another 360,000 nomistia annually.

The real issue that made Manzikert such a pivotal point in Byzantine and Turkish history was that Romanos' hold on the throne was had shaky from the start given that he had come to power essentially by marrying the widow of the previous emperor Constantine X Doukas. This act do not endear Romanos to the Doukas family, who used the fact that Romanos had been humiliated by the Seljuk Sultan to dispose of him and install Michael VII Doukas as emperor instead.

However, Constantine was a weak emperor who set off a chain reaction where in the imperial throne was viewed as being up for graps and generals abandoned the outer defenses of the empire to stake their claim on the throne. All the while, the main reason Romanos had instigated the Manzikert campaign in the beginning was to put an end to Turkoman raids coming from the east. While the Seljuks had little interest in the Byzantines, this did not stop still nomadic bands of Turks called Turkomen from invading Armenia and Cappadocia. Given that these areas were under the control of Byzantium and that the emperor had a responsibility to protect his empire and that defeating the Turks would help to stabilize his hold on power, There is little wonder that Romanos decided to undertake his campaign.

However, with the emperor defeated and the command structure fighting amongst itself, this provided the Turkomen a golden opportunity to enter the empire nearly unopposed and settle in a land similar to their Central Asian homeland. In a move reminiscent to how the Western Roman Empire had used Germanic tribes in its wars, many Byzantine generals started using the Turks, a provilent case being one Suleyman ibn Kutalamis who had aligned himself with the Governor of the Anatolic Theme (Providence) against Michael VII. The Governor was ultimately defeated but Suleyman took over the city of Nicea, which would be the first capital of what would be the Sultanate of Rum (Rum means Rome in Turkish and refers to the fact that the Byzantines still referred to themselves as Romans and their Empire as the Roman Empire).

It also be mentioned that the Turks were not the only people the Byzantines had to concern themselves with. In addition to conquering England , the Normans also conquered Sicily and Southern Italy from both the Arabs and the Byzantines, ending with the fall of Byzantine Bari in 1071. The Normans also served as mercenaries to the Byzantine generals and one Norman, Roussel de Balliou attempted to establish for himself an independent state in Anatolia before being defeated by the Byzantines.

The crisis brought on by Manzikert only started to come to end in end with the proclamation of Alexis Comnenos in 1081. He quickly married Irene Douka and appointed Constantine Douka, the son of Michael VII as co-emperor, putting an end to the civil war. However, Alexis's primary concern at the beginning of his reign wasn't the Turks but the Normans under Robert Guiscard, who saw that Alexis was a usurper and desired the throne for himself. Likely for Alexis, Guiscard's plans fell apart as a storm in 1081 and a epidemic in 1082 decimated Guiscard's forces. Regardless, Guiscard did make Alexis neglect Anatolia, as Alexis essentially kept Suleyman in power until he was killed in 1086 near Antioch. However, what Suleyman had started to form in Anatolia passed on to Kilij Arslan, who set his base in Nicaea after moving away from the collapsing Great Seljuk Empire that had defeated Romanos IV. It was that this point that Alexis sent a fateful letter to Pope Urban II for military aid that would set off the Crusades and ultimately seal the fate of the Byzantine or Eastern Roman Empire.

TL;DR: Romanos IV's capture and release set off a civil war in which the Turks both participated in and took advantage of which occurred alongside Norman aggression, which was considered a greater threat to the empire.