Big powers are neither good nor bad, they are just big, that does the trick. The rest is demagogy for the conquered subjects and the ordinary citizens.
In the case of the Federation, the Borg simile is just a metaphor, a way to ask how much of their political freedom, cultural idiosyncrasy, social conventions, and economic interests a small planet or ethnic minority should give away in order to become part of the Paradise. Speaking of realism, small worlds do not join big powers against their will, they join out of necessity and because the big powers usually instill supportive governmental structures that legalize the affiliation. When the Circle wanted to get rid of the Federation presence on Bajor, Sisko prevented it and made sure that the Bajoran government kept its pro-Federation orientation although he violated a direct order to leave the station. Still he was not reprimanded later because what he did was beneficial for the Federation.
I also find hilarious the quasi-religious conviction of the Federation fans who never question or analyze the makeup of the Federation but just insist on its rightfulness. Assuming that the entire universe consists of baddies and only the Federation and its affiliates are good is pretty childish.
In this sense, Sisko is a great character because he challenges the cliché about the sanctimonious Federation that never plays dirty. He is no angel, he has his grudges, his disappointments, his personal losses, bitter vendettas and dirty compromises. His clash with Eddington marks just another step toward his disillusionment. He adds much grittier and more realistic nuances to the usual heroic Captain model because he was constantly forced to overstep the limits of his Federation values.