How about you speak with some respect? Ad hominem attacks won't get you anywhere and will only detract from your points.
You do know he was running around, on top, and under the behemoth, right? Why didn't he run up the neck, over the head, and then poke the eye out from there? What can the beast even do to hurt him when he is in that area? Why not take advantage of the enemy's blind spot because of its damaged eye and attack from there?
All of these seem perfectly reasonable plans of attack to me, compared to, for example, forcing a crying, distraught knight to pilot a mech, using a large-scale spell to attack the beast (which has a flame breath attack, as you said, but didn't think to use it then) head on, and then jumping in front of its face to manually electrocute it? See why I can't accept "it is difficult" as a reason to not stab the other eye?
I find it strange that there is a need to defend this part anyway. It was clearly done to prolong the fight and to show flashier attacks. Why? Because that is what this kind of story is all about. It's not about efficiency or making logical moves. It's about what entertains the target audience (clearly not nitpickers like me). Blinding both eyes may have been the most effective method to win, but that also means it is boring and predictable.
So you see, I do understand why it unfolded that way. And like I said, I am actually just nitpicking, and that this isn't a dealbreaker of any sort. Why defend this? Just chalk it up to action fanservice, much like how the Avengers always choose illogical and inefficient ways to defeat random grunts when just hitting them with straight punches and front kicks would be faster.
The premise is ridiculous. Coding doesn't work like that, even if you are a genius. You can't just touch code you've never seen before, instantly understand it, and then rework it in the span of seconds (Yes, seconds. See how the mech became faster and faster? He clearly said he was reworking his code to do that. For that to happen, he had to be optimizing code he just wrote a moment ago, which makes you wonder why he didn't write the more efficient version in the first place. WTF.) Even a highly skilled developer will have trouble fixing a defect from code he didn't write, much more reworking a foreign OS. What this guy did is beyond ridiculous and was clearly thought up by an author with no IT experience whatsoever.
Imagine it this way. What if, instead of him stealing and reprogramming a robot on the fly, he had been working on his own unit before this incident, making him familiar with how they work? What if, he already had experience editing the code from a different mech because he was given a (convenient) chance to? What if he merely rewrote his already tried and tested code for the stolen mech this episode? How much more convincing and realistic would that have been?
But you see, this kind of show isn't about realism or making perfect sense. The way it played out reeked of lazy writing, sure, but it also had the most "WOW factor" and flashiness. It is almost expected for stories of this ilk and might even be intentional. At the very least, it is acceptable.
It's not dumb because I say it is. It is dumb for actual reasons, which I stated above. And please ease up on personal attacks (the one in bold). Also, just because it has dumb parts does not make it not entertaining or a bad watch. A lot of stories have aspects like this.