That's why I also proposed that the dynatoi lose big in a rebellion so that my hypothetical emperor can break up their estates and give the themes a second wind for a while. Also Bulgaria was pretty soundly beaten by Basil so I believe their border in the west is relatively secure for now while the emperor could theoretically avoid Manizkert and a fight with the Seljuks in a number of ways.
Also while I'm not a military expert, what I'm proposing is that the Byzantines create a Marine corp to project force rapidly wherever needed and use viking style tactics to get behind enemy lines and harass them until a larger force can arrive.
The problem is that even if the dynati are broken, any Emperor who switches attention away from the army is going to be inviting defeat and invasion. Whilst a frontier might be temporarily pacified, such peace would never be stable, and sooner or later a strong adversary would (re-)emerge. A raiding naval force could work, although even then I think it would be used as an adjunct to the army, rather than becoming the senior service in its own right.