Flaws empower characters. This is an unavoidable fact of the system. Unearthed Arcana tries to deal with min-maxing by making flaws the negative of two feats:
Flaws are generally bigger in magnitude than feats. That's because players always choose flaws that have the least impact on their characters, while taking feats that have the most. For example, while a feat affecting skills grants a +2 bonus on two skills, its counterpart flaw might impose a −4 penalty on two skills.
Basically, the authors of Unearthed Arcana understood that players would be drawn to flaws that don’t penalize things of great value to them, and use the bonus feat to get benefits that are of significant value to them. That’s natural, and frankly not even meta-gaming—a real person with real flaws is also likely to focus on endeavors that are not unduly penalized by their flaws. Someone who is color-blind is not likely to go into business selling subtly-different shades of paint.
But the authors of Unearthed Arcana were either unaware, or refused to acknowledge, another important point: a lot of feats are crap. Those feats that give +2 to two skills? They’re awful. A character should never take them.1 They’re not worth even half a feat. So doubling that bonus as a negative doesn’t really represent a fair cost for a bonus feat—even before min-maxing is involved.
So flaws as a system empowers characters. They’re a substantial advantage over not taking flaws. Even when you aren’t going out of your way to game the system. That’s just the way things are. I’d call it a problem, if I weren’t too busy calling the lack of early feats a problem in the system—which I strongly think it is. Humans are the best race in the game for almost everything solely because they start with 100% more feats than everybody else—watering that advantage down by making them have, say, only 33% more (4 instead of 3) goes a long way to improving balance. Plus it helps a lot with the system’s myriad feat taxes. And flaws can be fun!
As for Murky-Eyed and Blind-Fight, that is not a particularly abusive combination. For one thing, Blind-Fight is a kind of mediocre feat—it’s not awful but really, miss chances are bad enough that you’re going to want to do better than simply rolling twice, whether that means supplying light, banishing darkness, getting out of the fog, or seeing through illusions. And Murky-Eyed is a really brutal flaw—there are plenty of flaws that are simply much less negative, like Noncombatant or Shaky in a ranged or melee character, respectively. Plus, as you say, the flaw and feat go together really nicely—it makes perfect sense that a character with really bad eyesight would train to fight better when they can’t see well.2
Really, my concern is more, what actually happens when you have both? You roll twice when you might miss, and fail if either die fails—and then you get to reroll. Do you have to reroll two dice again? Or just a single die, and only have to succeed on the one? Or do you get to reroll one of your two dice—pointless if both failed? I have no idea. None of these approaches is particularly powerful—the flaw is mitigated somewhat, but hardly obviated. Honestly, my preference would be for something that actually isn’t possible by the rules, but would be how I’d go for speed of play: I would have you roll three dice and have to succeed on two out of three.
I would welcome such a character; if anything, I’d be concerned that you may have gone a little overboard with the flaw and were hurting yourself too much. As I said, flaws generally empower characters—I would expect other characters to have benefited more from their flaw and bonus feat than this.
Barring prerequisites, but frankly very few of them are actually used as prerequisites anyway.
Though it arguably makes more sense that they would avoid sight-based combat altogether—but maybe the Murky-Eyed flaw came from an injury or disease later in life after they’d already committed to a more martial path. Or maybe they had some other reason to be stubborn about it and fight that way despite their poor eyesight.