I'm not entirely sure what you are referring to, though I assume it is the reaper virus. If that is the case, then we need to remember that Reapers can also easily dominate the minds of organics as well. But like you said, there's no way Quariuans can developer a virus on par with the Reapers anyways. The most significant progress they made towards hacking came from Tali's father, and his work completley backfired on him. So I don;t have muc confidence in Admiral Morrigan's crazy plan to hack the Geth. Though its not really any more crazy than Admiral Loghain's plan to zerg rush the Geth. I find it funny how he brags about how powerful the Quarian's fleet is, when in reality the majority of their fleet is composed of scavenged ships that need constant maintenance to stay in barley operable condition. Meanwhile the Geth have highly advanced technology that can outmatch the advanced ships of the races that actually matter.
]I think they failed a fair bit anyway. Even if the quarians are meant to be dumb, their leaders' plan is so dumb that it's a wonder they ever managed to get into power, or keep the fleet alive for more than about four days. But I get the horrible feeling from a lot of the dialogue that you were maybe supposed to sympathise with the quarians. Advising them to attack the geth or leave the geth alone is presented as a moral choice. Regardless of whether you think the quarians deserve their world back or not, the war would be so transparently suicidal that the answer should be obvious. It's basically a choice between "quarians don't attack the geth" and "quarians all die pointlessly". And remember that the least sympathetic admiral on the board (the one who is most keen to convict Tali) is the so-called "geth apologist". It does strongly suggest that the writers though it might actually be considered a good idea.
I know what you mean, but I just can't bring myself to accept the idea that the writers would actually have the Quarians win that war. It wouldn't make any sense based on the established story. It doesn't matter how badass Shepard is. He can't make magically cause a fleet to be a thousand times more effective. To be honest though the whole trial is really weird from a moral perspective. Tali's dialogue clearly paints showing the evidence as a bad choice, yet decisively good things come from it depending on your viewpoint (example; Admiral Morrigan having virtually no public support for her stupid hacking plan). When you consider that the
paragon choice is covering up the death of a dozen Quarian scientist and marines just to please Tali, that whole mission seems to be twisted.
As for how those idiots got into power.,I choose to believe that being an isolated nomadic society for several generations has fucked up the Quarian political system. I mean Tali, a young Quarian with no political experience or leadership skills whatsoever, is apparently being considered for a a position on the admiralty board.