To my knowledge there is no actual information on how legendarys will be released yet.
The current speculation is that they will be implemented as raid bosses, meaning everyone with a gym close by will be able to go and raid with others regardless of their lvl or gym activity (before or after the update).
Also possible would be that having a gym badge maxed out might affect your ability to catch / raid legendarys, so you'd still only have to have at least one gym close by, that you regularly visit before you can catch a legi.
Anyway, with how Niantic has been dealing with botters and spoofers so far, I doubt they could afford to give them even more of an unfair advantage. The old gym system definitely seems irrelevant to the new one, it seems like this will be a fresh start for everyone regarding gyms.
But as mentioned, this is all speculation. Rural players will always have a slight disadvantage as opposed to urban players (just looking at the number of people playing in cities, it will be so much easier to take out a raid boss in a group of 10 than in a rural area with just one or two friends who are playing) and I don't think this will change that quickly, but I like to belive that Niantic will not add to that disadvantage by making legendarys dependant on how many different gyms you are holding.