Against Terran specifically, you should attack the SCV as it is building since that is the weak link. It will go down quickly and then you will not have to worry about it any more.
Zerg players using this tactic will often cancel the extractor as it gets close to finishing and start it over again, to maximize how annoying it is since the health of the extractor resets to maximum every time. In this case, at least he cannot grab both geysers.
Protoss players can build assimilators on both geysers fairly easily, but it's at a cost of 75 minerals each so you will be able to get out an extra zealot and a half that he won't have access to, giving you a slight army advantage first until you get the assimilators away.
Overall, the main thing you have to do against this kind of tactic is make sure that it doesn't affect your macro. Keep building probes nonstop to mine minerals as fast as possible, and possibly go for a 2-gateway or more build to pump out zealots as fast as possible until you've dealt with the issue.
Do you want to know how someone can lose or how he did lose?
Bly lost because he played very poorly: he did not build enough drones.
Take a moment to let that sink in, because its a very very big mistake and its the difference between a good Zerg player (like Fruit Seller) and a bad Zerg player (like Bly).
Instead of backing off after taking the Terran Natural, he continued to press in. He sends wave after wave of a consistently sized army. He does this because he's not building more drones so he cannot afford a larger army. By comparison Tarson's army gets larger and larger after every wave. He's able to continue to accumulate units because he has a fairly healthy economy. This is due in part to MULEs, but largely because Tarson built enough SCVs. Even after losing his Expo he still has as many workers as Bly does. Think about that for a second. He lose an entire base and all his workers in it and he still has more workers than his opponent.
This game could have easily been one that was featured on Day 9's Newbie Tuesday
I could point out a dozen mistakes that Bly made, but none of them matter nearly as much as his poor drone usage. Because of his lack of drones, his assault becomes almost an all in. So in response to your question How is it possible Zerg with biggest advantage can still loose to Terran? Bly didn't have a big advantage. He sacrificed his economy on a gamble and it didn't pay off.
But let's imagine another universe, where Tarson wasn't playing Bly but was playing against a better Zerg like IdrA; and let's assume IdrA made the same early push.
Now IdrA is sitting on 2 bases to Tarson's 1, but they have equal workers. So instead of continually pressing his advantage, IdrA decides to play like he always does: Macro. He sits back and takes a third base and powers drones. Tarson retakes his natural and now he's down 2 to 3 bases. Not a big advantage for IdrA, but remember a Zerg can make drones faster than a Terran, so it takes Tarson longer to saturate that 1 base than it does for IdrA to saturate his 3. Now IdrA has a huge economy and he goes Roach/Hydra (or these days he's favoring Muta/ling, but pretend).
Imagine that battle for a second... or don't, because it actually happened. IdrA knocked out Tarson in IEM, exactly like I described.
The smartest thing you can do in Starcraft if you are ahead is to get more ahead. Anyone who played seriously in Broodwars knows this because if you pressed like Bly did, you got destroyed 100% of the time. Now Starcraft 2 is still new so a lot of people feel like they can do crazy 2 base play, but if you look at the high end GSL matches you see less of that and more of people trying to get more ahead.
You also mentioned a quote talking about Marauders vs Banelings. Now I don't think that the relationship between these two units had anything to do with this loss, but let's talk about them for a second.
Banelings are a highly specialized unit. Their role is to act as Zerg splash damage on light units. By comparison the Marauder is a more generalized unit, designed to act as a Meat shield (much the way the Roach acts for the Zerg). So it makes sense that a Baneling doesn't function well against Marauders (as that's not their role), and it also makes sense that Marauders do a good job of preventing Banelings from striking other units (as that's their role).
I would hesitate to say that a unit is broken because its functioning in its role and another unit isn't functioning in something outside its role. But let's say you want a way to deal with MMM balls. Instead of sending it waves of Banelings on their own. Consider mixing in more Zerglings (Bly actually does this to large effect). Now let's vary our composition based on their unit mix. More Marines? More Banelings. More Marauders? More Zerglings. Can't find a good place to engage? Burrow/Drops/Fungal Growth/Wait and Flank.
Here is the key thing, none of this is any assessment of Banelings against Terran, but rather an assessment of the tactics used.
Best Answer
You essentially have a few options if you scout a forge fast expand.
Try to out macro them (Defensive) You can play the long term macro game, take a 3rd and out produce him. Because he is going for an economic opening it means that he won't have a strong army so you will be free to drone hard like you say you are. However it sounds like you might be missing injects and not having enough larva to fight the protoss army. Either work on this mechanic or drop a few extra macro hatcheries so that you have some extra larva that way.
Constantly be scouting them so you aren't caught unaware of what they are doing. If you see a stargate you know they are going some type of air play and should be getting appropriate units to match once you know what they are getting (ie. know the difference between getting mutalisks or corruptors), or maybe they're just rushing carriers/mothership. Make sure you scout often because knowledge in this game is vital.
Pressure/All-In(Offensive) There are several kinds of pressure/all-in strategies that you can do if you scout a force fast expand.
You have your traditional baneling bust which will work if they don't have enough defense. You follow this up with lots of zerglings and destroy their workers.
There are variations of a Roach Rush designed to kill/pressure the protoss player if they get too greedy.
You can also use mutalisks to pressure their mineral lines because they will have a large amount of their defenses located at their choke point. This will leave you free to kill probes and get you another economic advantage. After they sufficiently defend this, either with cannons or blink stalkers it depends on how many mutalisks you have. There is a critical mass where you can have enough mutalisks that they will one shot cannons and they won't even matter. You should have a transition out of this.
Your late army composition should consist of infestors, zerglings/roaches, corruptors and broodlords if you play a longer macro game where you can get to these tiers of units. Of course your army composition should be reflective of what you see your opponent getting. For example, if they don't have colossi, don't have corruptors.
Targeting sentries will make your army stronger as it is a very gas heavy unit for them and will cut down on their higher tier units if they choose to remake the lost sentries. Lost sentries also mean that they cannot control most of the fight. What I mean by that is that they cannot force field off parts of your army during an engagement thus making your army weaker.
If you let a protoss get up to an optimal army composition, they will crush your army. A maxed tech protoss army will generally beat a maxed tech zerg army. You may be able to remax quicker and overwhelm them, but proper control from the protoss player will cause you to lose. A combination of storms, colossus, force fields, and archons with some zealots and stalkers plus a mothership will decimate any zerg army.