The blindness is the problem, not the Flyby.
Considering how crippling a permanent blind condition is... This just seems like a really powerful strategy
Yes, I agree. Blindness is extremely crippling. Which is why there is a core rule that shuts down this kind of strategy. The rules for Damage and Healing state:
The loss of hit points has no effect on a creature’s capabilities until the creature drops to 0 hit points.
Sight is a perfect example of a capability that suffers no effect from damage. So if damage can't blind a creature, what can? Only abilities that explicitly say so!
Ows have no such ability, hence they can't blind an enemy, at least not until that enemy drops to 0 hit points!
On the other hand, Flyby contributes almost nothing to the strategy that you have described, because a creature can't take opportunity attacks if it can't see its enemy. In other words, anyone can safely back away from a blind enemy, whether or not they have Flyby.
Moreover, consider that all the options available to players to blind enemies mid-combat consume some kind of resource (i.e. spellslots for blindness/deafness) and even then, the blindness typically lasts only a couple of turns.
Strategies against Flyby
If you set aside the blindness, it becomes clear that an Owl is basically useless for combat1. A druid that is high enough level to turn into a flying beast would become a Giant Owl, a Pteranodon, or (if they are a moon druid) a Quetzalcoatlus. Like the Owl, these beasts have Flyby and unlike the Owl, they actually pose a threat, especially the Quetzalcoatlus. Therefore, the question of how to deal with Flyby is relevant.
In the case of a Giant Owl or Pteranodon druid, the best strategy is probably to ignore them, because druids deal more damage if they sling cantrips and spells. Of course, that is only true if the druid is not doing something notable (like concentrating on a powerful spell) while in the shape of a Giant Owl or Pteranodon.
In general, the best way to deal with enemies with high mobility is to use ranged attacks or magic. For example, magic missile doesn't care whether the enemy is 5 or 80 feet away.
The next best way to deal with enemies with high mobility is to rob them of said mobility. Nets, grapples, and magic all do the trick.
The worst way to deal with enemies with high mobility is to ready melee attacks, because a readied action is a wasted action if the trigger does not occur. Any creature skilled in hit-and-run tactics will know not to approach an enemy who has done nothing on it's turn. Moreover, readied attacks cannot benefit from multiattack nor extra attack and readied spells require concentration, so the Ready Action is typically a losing move even if it does trigger.
1 The exception being the notorious Owl familiars.