In this particular context, Free Will means self-determination, i.e. the right of the population of a planet or other celestial body to choose the course of its own evolution. This is an important aspect from the point of view of interstellar (or even intergalactic) ethics.
This is where Star Trek's Prime Directive comes into play. In Star Trek itself, the Prime Directive states (among other things) that no contact shall be made by the United Federation of Planets with any civilization that has not yet attained warp drive capability. Transposed to our own present-day Earth, this means that, even though there are and have been breakaway civilizations and there are secret space programs, the vast majority of humanity is still left in limbo over whether there would be intelligent (and even space-faring) life on other worlds, let alone over whether warp drive technology is even possible.
Now, of course, anyone with a brain would be able to ascertain that the mainstream means which are used for searching for extraterrestrial life are suffering from tunnel vision to the degree of ludicrousness. Even "3D" beings from elsewhere in the galaxy might be a few thousands of years ahead of where mainstream science is on Earth today -- it doesn't even have to be a million years, or a hundred thousand years, no, just one thousand years. We already know that radio wave transmissions are a very poor means of conveying information over longer distances, but still, that is what SETI is looking for. And mainstream science still believes that the laws of physics of the universe are centered around gravity, while there is clearly an electromagnetic component to it all.
As an illustration of this, in the 1990s, a Mexican scientist by the name Miguel Alcubierre theorized a warp drive which would bend spacetime around a spaceship, while the ship itself would remain stable and stationary in a bubble of flat spacetime. However, it has always been assumed that dark energy and/or dark matter were needed to accomplish this. Recently however, a retired physics professor from Omaha in the USA has begun working on a warp drive in his own garage, based upon the use of high voltages to create a warp bubble, and his experiments appear promising. He has so far already been able to compress a laser beam, showing that he has, indeed, managed to warp spacetime.
I couldn't find the original video anymore where the retired professor himself explains how and why he came to these findings, but the ~6-minute video below does explain it all equally well...
https://www.youtube.com/watch?v=eFUeWNuSBLw
To return to what I was talking about higher up however, as far as the mainstream population is concerned, we're still at the stage where we think that we might possibly be the only intelligent creatures out there, and that the fact that we have intelligence is merely a fluke of nature, caused by random genetic mutations. And on the other hand, we've got the religious people, who say that the scriptures don't mention anything about life on other planets -- you have to keep in mind that it was these very same religious institutions who insisted that Earth was flat, and some of them actually still do.
Ergo, an open and public intervention from ETs in our way of life down here on Planet Earth would have significant consequences to our evolution as a species, and can therefore not be allowed in the ethics of benevolent and advanced ETs, wherever they come from. They can make themselves visible at times via entries into our atmosphere -- and sometimes they need to, in order to make contact with members of their own species who have incarnated on Earth and have agreed to becoming contactees in order to pass on messages -- but there is always plausible deniability, because no formal contact has been made yet.
Now, the interesting part is that even the negative ETs have not made any formal and open contact yet -- semi-formal, yes, through secret meetings with selected government officials, but nothing that was both formal and public -- but I doubt that this would then be a matter of ethics on their part. I would much rather think that if they were to simply come down here and seize the planet, they would get their rear ends kicked right off of the planet again by The Good Guys™.
So what we have here, is a chess game. There is interaction, and even intervention -- the latter at the spiritual and for humans mainly subconscious level -- but no physically tangible large-scale and overt contact. It's a very delicate situation, in which several ET factions -- whether good, evil or anywhere in between -- are constantly walking a tightrope on what they can get away with without completely upsetting the balance. The Good Guys™ because they respect our Free Will, and The Bad Guys because they don't want to get themselves into too much trouble with The Good Guys.