It doesn't matter how old Yoda is. He still makes mistakes and he was wrong about a lot of things.
He didn't believe that the Sith had taken over until it was too late.
He didn't believe it was possible to turn back from the Dark Side.
He at one time (like his colleagues) used the Force for attack and participated in wars, then later changed his mind and taught that those things were not part of the Jedi lifestyle.
He wanted Obi-Wan to kill Anakin, when in fact had he done so, the prophecy would not have been fulfilled (only as it turned out). He also wanted Luke to kill the Emperor and Vader, and yet that's not how it turned out. He justified this by his belief that Anakin was "gone... consume by Darth Vader" when in fact Luke proved that there was "still good in him."
He thought that Luke would "destroy all for which [Han & Leia] have fought and suffered" if he went to face Vader on Bespin. That didn't happen.
He ran away from Sideous when it seems like he could have continued the fight and went into exile for 20 years.
He foolishly decided to split up and take the Sith one on one instead of joining together with Obi-Wan to defeat them 2 to 1 with better odds, why?
He missed his chance to stop Dooku by tossing that giant pillar onto Dooku or using it to disable his ship, instead of levitating it in the air for no reason (or just force pushing them out of the way of the pillar and going after Dooku), thus prolonging the war which lead to countless more deaths.
And so on and so forth.
I'm not saying that Yoda NEEDS to be perfect or infallible. But I think people are assuming that because he's one of the good guys, because he's a Jedi Master, and 900 years old that he WOULDN'T make a mistake.
Yet we see that he's made tons of mistakes and is just as fallible as any other character in the saga. Obi-Wan makes numerous mistakes as well, as does Mace Windu, and all the other Jedi. Palpatine makes mistakes too. Luke makes mistakes, he just happens to be luckier than some of the other characters.
I think it's a mistake to say that there is no Dark or Light Side of the Force, since this is always how it has been in the Star Wars mythology from day one (well, technically it isn't the "Light Side" that is just what the normal "good nature" of the Force is called in the EU, for convenience thanks to the video games.. in ROTJ, it is simply called "the good side").
Vergere in the NJO is revealed to have been full of crap, telling lies and having opinions that were based on a biased POV.
There most certainly IS a Dark Side. And it is evil.
However, that doesn't mean Jedi are perfectly good, just because they aren't Sith or don't use the Dark Side.
The idea that a certain power is always Dark Sided on the other hand, does seem to be a mistaken impression, and that's what I'm arguing.
Force Lightning need not always be a "Dark Side Power" that you have to tap into the Dark Side to use.
On the other hand, in the EU, it seems pretty easy to fall to the Dark Side and pretty easy to turn back from it, and it seems like "Good" characters regularly "skirt the Dark Side" and seem none the worse for wear. So judge that as you wish.
I think by the movie standards, users of Force Lightning may tend to be Dark Sided, but "Good siders" can also use it if they are sufficiently powerful, they just tend not to favor it.
By EU standards, using lightning may be "Skirting the Dark Side" but since it's so easy to come back from the Dark Side, perhaps these "Light Siders" don't find it that big of a risk. Sort of like if drunk driving could only result in a paper cut. More people would probably risk driving drunk, than if it often resulted in death or crippling injuries.