I really don't feel that strongly about any of the points you are making here, frankly.
For a start, I have no idea what makes you think that the Githyanki patrol is presented as "an obvious solution". If anything it seems to me that it's presented as one out of multiple options (and one several of your companions express open skepticism about, on top of that) and it turns out to be one of the most misleading ones, since the outcomes range from "You get nothing, good day sir!" to being brutally stomped. At no point it turns out to be an "obvious solution", just a false option.
Second, "We shouldn't concern ourselves with the refugees is ALREADY a point that pretty much all your companions aside from Wyll make to you, and in most cases unless the player deliberately chooses otherwise you somewhat indulge in doing something about it just as a tangent to what at that given moment is your main goal ("Find and meet the druid, ask for his help").
About the goblins, you are offered MULTIPLE alternate options to infiltrate their camp that do not involve massacring the guards. That aside, the implication is not that if you kill the guards "everything is peachy", but that you can infiltrate the temple with its occupant unaware of the battle you just had on the outside.
Last but not least, the characters DO "hit a brick wall in dealing with their infection", given that every single path to a cure turns out to be a false lead and the only thing keeping you alive past the first two days is the peculiar nature of your tadpoles.
Part of the issue is that the gameplay and plot disagree on what the rails should look like. The plot leads you straight from the start into a fight with a party of level 5 enemies while you're still level 2.
Well, that's a different issue altogether, isn't it? One that incidentally we were already addressing in another topic.
