In patch 4.3 Blizzard introduced an automated system that allowed guild members of guilds whose leadership no longer played to take over their guilds. The way it works is that if your guild leader has not logged in within the last month anyone of the highest guild rank that has anyone who has logged in within the last month can take over the guild. There are plenty of folks complaining about this of course because they spend years building up their guilds, recruiting, raiding, etc. and after taking a long absence they have discovered that some random.dood has taken over their guild. I don't have much sympathy for them to be honest. The system isn't set up badly at all - if you have trustworthy friends still playing you can simply promote them to the second rank and nobody but them can take over the guild if you take some time off. The only way the guild falls into the wrong hands is if you stop playing and have absolutely nobody in the guild that you trust that you can trust to log in that you can put into the second spot. Even then you can always guarantee your guild by booting everyone out if you really want!
This happened to 'my' guild OGT. Pretty near all of the officers stopped playing completely earlier this year and one of our longtime WOW friends logged in and was handed the guild. He had no intention of staying on playing for very long though and so in another couple of months the guild will be up for grabs once again. This doesn't much bother me really as I don't intend on going back but also because if I don't use a thing I don't see why it should be kept for my use alone. I put as much work into running OGT as anyone and for years it was my home away from home but I don't feel like there is any reason that I should own it forever. OGT was a community space that we worked hard to make a great place to hang out but that great place was a combination of people and ideas, not a name. If all of my friends decided to start playing all over again we could create a new guild and get everything back in no time, excepting of course the guild perks that we would have to earn once again.
I think guild leaders have a sense that they own a guild in the same way they own a shirt. That just isn't an accurate representation of the situation though because so much of what the guild is is a function of all of the members. The leader is very important of course because they have a lot of power and can set the tone of the place but in the end a guild is a place with many members all of whom contribute. A guild can become completely nonfunctional if there is no one in charge to set permissions, organize ranks, invite/boot people etc. so it is important that such abilities are available to someone who can use them.
If a former guild leader comes back and wants their old position back the simplest thing to do is to earn it. *Be* the guild leader. Do everything that a guild leader does aside from have the title and have the power and either you will get back into a position of power once again or you shouldn't be a in a position of power once again. That might be because the new members don't want you there or because the new leadership doesn't trust you but either way if you can't become the leader by being the leader then either accept the new position or move on.
This is a simple case of wanting to have your cake and eat it too. You can just remove people from the guild and remove inviting privileges to prevent people from taking over - no one is going to take over my alt's banking guild! What you can't do is maintain a thriving community that you can come back to as the emperor any time you want. Either give up the guild or be part of the guild, one or the other.