It depends on what the original idea for the Borg was really, in "Q Who" they didn't seem to actually assimilate any cultures, just their technology. Then from "The Best of Both worlds" it's implied that the Borg have seemingly altered their outlook, suggesting that from now on due to the Federation's mere existence and influence, the Borg will now forcible assimilate everyone they meet.
In this context you could argue that the Federation is merely trying to correct an issue they may have been responsible for in the first place, and destroying the Borg would be the lesser evil in this instance.
Of course this all goes out the window by the time of "First Contact" and "Voyager".
Yes, ultimately the Federation and the Borg are at war, the Borg's single mindedness in how and what they do to achieve what they believe is right is going to keep this "conflict" going. The Borg believe that they're improving those they assimilate, in a perverse mirror version of what the Federation does.