In TNG everyone felt everyone was too comfortable with each other, all friendly and not really arguing. They added Ro Laren to 'throw a cat amongst the pigeons', someone to add a little more atmosphere to the crew interactions.
I think Seven was a similar idea, everyone respected Janeway and she always got the last word generally, Seven questioned her authority regularly and allowed the human side to Janeways character to come through on several occasions as she helped Seven regain her humanity. Kes did this to a certain extent but it was more Janeway teaching Kes little lessons about life rather than batting horns to get a point across.
Seven also replaced Kes with her interactions with the Doctor, a great pair in my opinion. Was nice to see how Kes taught the Doctor what it's like to be a person, then the Doctor did the same for Seven whilst enhancing his own character.
I can see your point in that Seven was similar to Tuvok and Data, and a more innocent viewpoint was lost with Kes leaving the series, but saying that she had very few good episodes in my opinion, maybe it was being so closely paired to Neelix, would have been interesting to see more of the Paris-Kes thing.
So, to answer your question, in my opinion, Seven was the right choice at the right time.