See, the problem with advisors is that, with a few exceptions, most have their own agendas and want to further themselves or their family. We see it in King's Landing with Varys and Littlefinger. Skahaz mo Kandaq, for example, is head of House Kandaq, an impoverished house that has been trod on by other noble Meereenese families for centuries (remind you of anyone else?) If Dany followed his advice to slaughter the innocent children then House Kandaq would stand to potentially grow their own power and wealth exponentially. That's not the only possibility of course, there are far better theories about what Skahaz's goal might be but this is the easiest to explain for example's sake.
And on the topic of Skahaz's eagerness to kill the children, ignoring the aforementioned, what purpose would it serve? The Meereenese plainly don't want Dany or her dragons ruling them and as cruel as it may sound sometimes you just have to take a hit to win the war. Dany took one child from each questionable family (there's likely many more who are better at keeping secrets), if that child dies then, well, them's the breaks. It might deter some of the more sentimental nobles but Dany's rule has stifled the Meereenese economy and effectively destroyed their way of life, a life that is built on the back of slaves, and that's not something that can be changed overnight, see: the CSA and the American Civil War.
On top of that Dany just doesn't know how their families will react. It could very easily harden their resolve to see her dead, for instance. It could also increase the Harpies' numbers. Tyrion in the show, I'm not sure on the books, has a great scene with Cersei after Joffrey orders the murder of Robert's bastards. He essentially says that she was foolish to let it happen because she gave the enemy their rallying cry, "The Queen slaughters babies". The same would happen to Dany no doubt.
Yes, she should listen to her councillors more but forging her own path isn't necessarily wrong either. If she relies too heavily on councillors she risks becoming another Robert, if she does everything herself she risks becoming Maegor I. She has to find the middle ground and I sincerely hope she will in the coming books.