Honestly though, I don't see Diogenes having the political acumen to actually get rid of the Doukai. He is more likely to squander his political capital on a eastern campaign (we agree till that part) that would turn into a disaster. If he is smart-he'd play divide and rule and a client state in N.Mesopotamia would be great-but I doubt the Empire has the means to actually achieve that at that point in time.
If Diogenes was smart he'd hold off from doing anything stupid and actually work on getting rid of the Doukai-marry a Bryennos or Komnenos to get their support maybe? Im likely being unfair to the guy but he'd likely overextend and either die in some ditch in Syria or be disposed off by a coup. I also don't think Alp Aslan being captured then would be very damaging-man died within a year of Manzikert OTL and the Seljuks still did OK.
(I may also be biased since I just reached Manzikert in my own TL-hopefully my thoughts have not seeped in too much
)
To be honest, I'm trying to make an assessment based on minimal information and inference - we only have 3 years of a reign, and the PoD is his disaster that built his reputation for us. Switching that on its head leaves us a bit short on "who was this guy and what was he capable of" - makes good TL fodder. I see this as a chance for a good boring reign once he gets his house in order.
I actually directly disagree on his strategy, because even he saw that he had little to no political power in Constantinople, partially because of his policies (which tbh, the Byzantines sorely needed at this point, less dross, more savings). As a result he needed a war, and if he won it, he could remove his enemies. The people and the army love a winner in the field, especially if he brings home loot. Using his fiscal prudence and an anti-corruption campaign could well bring the army on side (if not some of the old generals) and cement his rule after a victorious war, allowing him to get rid of the Doukoi, and set the stage to bring the Komnenoi and the Bryennos onto his side, if they haven't been alienated by corruption charges.
I think we'd not be able to see either of your proposed alliances without some more success in the field - having Alp is a great prestige boost, not as great as the reverse was a prestige loss, but certainly enough to garner some respect for the Emperor. Until then, the Doukoi are still the better option. Get rid of the Doukoi, and suddenly house Diogenes is the best house to marry into.
I think a successful Diogenes would make a political alliance with the Komnenoi, and through them the Bryennos. Alexios served under him, and if they are both regularly in the field, Alexios may well make not only a good officer, but a later ally to marry a daughter to. (If the situation gets as such, he might become a particularly effective co-emperor as well). If there is an alliance there, I think he'd be a prime candidate to promote to the frontier - either to re-institute the Katepanate of Ras, or (my preference) reconquer S.Italy from the Normans. With a cleaner, more reliably paid army - and the money to turn Normans over to the Roman side, that would keep Alexios very busy, and help Diogenes, either by getting rid of a capable rival, or giving him S.Italy again, under a capable commander that would be able to turn Italia into a net gain. That could be repeated in Serbia (or reverse the positions) with Bryennos as his lieutenant in Serbia to become Katepan of Ras. Which leaves Diogenes with a much cleaner house to work with, so he can focus on using his not civil-war-torn Empire to strengthen it anew and take advantage of whatever piecemeal conquests he can.
Admittedly, this is an optimistic (I'm not saying best case), I'm assuming that the Komnenoi aren't about to try and seize the throne from Italy, and same with the Bryennos. But I think we'd see a reign defined by Diogenes, but well known for the Katepans of Ras and Italia, and their successes, with the moderately improved health of the Empire as a whole. Bit boring, no great conquest of Egypt, but instead smaller conquests of the Levantine coast. A good position, but not a great one that a bad heir, messy usurpation, or massive Seljuk invasion couldn't ruin - but I think the latter might be avoided - the Byzantine Paper Tiger hasn't been exposed, and has been made a bit more substantial by his reign, which may be enough to have Malik-Shah continue as per normal, without invading Anatolia - and collapse into civil war later. Boring, but good - exactly the sort of Emperor it needs at this moment. Egypt can wait for the next Emperor.