I think that ship has long since sailed. The Federation has always been portrayed as a benevolent imperialist state with plenty of colonies and protectorates.
Well, the sense that I always got was that its colonies were settlements created on uninhabited worlds by the Federation, with Federation citizens forming the new colony's populace, not oppressing or displacing any native peoples -- and with the colonies themselves being an intermediate step towards the formation of a new Federation Member. Deneva and Cestus being examples of colonies that became full Members in their own rights, for instance.
As for protectorates -- that's a bit different. A protectorate is still a sovereign state, it's merely one that a more powerful state has agreed to defend from external threats. They don't get to send representatives to the more powerful state's legislature, because they aren't in any way part
of that more powerful state. They still have absolute sovereignty over their own affairs, and can terminate the relationship at any point. So that doesn't equate to Federation imperialism at all.