The empire was definitely in a weird spot, but I think OTL scenario was literally the worst outcome possible. Defeat against the Seljuks, civil war, a competent emperor overthrown and the Seljuks taking Anatolia anyway. I don't see all of them taking place anyway if Doukas is not there to screw up Manzikert. Even if he feels comfortable enough to launch a civil war, I think the scale would be tipped in favour of Diogenes this time (who is still in control of the entire eastern army). More people (especially in Anatolia) would be more likely to side with Diogenes if he is victorious against the Turks. If the empire avoids ten years of civil wars (with two new contenders appearing when one is removed), unrest and people trying to establish their own kingdoms with the use of turkish mercenaries, the empire can definitely keep the bulk of Anatolia.
Hmm, I agree that Romanos would probably be in a more advantageous position, but he also was in one IOTL, and his downfall was caused more by mistakes he made (such as not capturing and holding the Cilician Gates or not attempting to capitalise on the temporary disbanding of the mercenary army of Constantinople in early 1072 iirc). So Romanos can again find himself cornered and forced to concede. However, with him being victorious, the Doukai (particularly Ioannes) may be less willing to blind him out of fear of sparking popular discontent, so perhaps they would force him to become a monk.
As for the invasions, again, I am not so optimistic: if no treaty had been concluded, the Seljuks would probably seize the opportunity to resume their raids in Asia Minor; if a treaty has been concluded, then things would probably develop roughly like OTL, since Alp Arslan could consider the treaty null and void. So I am not sure whether much would have changed. However, if the Doukai makea show of being in control of the situation and Mantzikert had been a victory for the Byzantines, the the Seljuks might be dissuaded from doing anything and decide to continue the peace with the Byzantines and turn their attention south towards Egypt.