That would make it the exception to the rule. I believe it is ethical to look at other alternatives before wiping out an entire species, however, if that species has no effect on the ecosystem and its mere existence only threatens another species; it should be removed.

Eg. Shark culling is not ethical as it causes more harm than good. In fact more people die from drowing than they do shark attacks. On average 7 people die worldwide from shark attacks, so it is not ethical to kill off millions of sharks to prevent further human casualties. To prevent such casualties, it would be best to educate people (do not swim where the water is murky etcetera). Shark attacks are essentially media hyperbole. Shark culling also tends to lead to other marine life to be harmed in the process as well as the ecological problems that arise from such methods.

Generally the easy way out is just to kill something without considering the consequences in the grand scheme of things.

The Guinea Worm on the otherhand does not factor in the ecology, so I would say that removing this particular specie is in fact ethical. 

Well, as its larvae live in freshwater outside the human body, it would factor into the ecology somewhat. The larva, for example, infect copepods prior to human consumption.

It essentially kills copepods and infects people. There are other animals within the ecosytem that eat copepods, so by removing the guinea worm, this would not create consequence within the ecosystem; nothing eats the guinea worm for survival. It is simply a being that does not offer any virtues; all it offers is death.
Killing it is certainly ethical, especially considering how some countries are plagued with them. 
Want some water to survive? Nope - this sucker will teach you a lesson for trying to survive.

that's what higher organisms will say about humankind one day

I was thinking more along the lines of the kind of large scale water cleansing we have in more developed countrys, instead of pouring insecticide into peoples drinking water. I know a lot of countrys use chlorine among other things, but where I'm from they mostly use a long succession of diffrent micro filters and micro organisms to mimic the way groundwater gets cleared and it works really well. (Also chlorine makes me sick, so I can't drink, for example, spanish tabwater)

Your point still stands, the worm would likely die out, but not due to planned extinction, but though passive behaviour change of humans.

Think of it this way, Lions are stationary predators with large hunting grounds. Antelopes move around the continent in search of fresh grassland. The antelopes move through the lions hunting grounds, were they get decimated greatly every year. The lions have to stock up fat for the dry season when no suitable prey will come through their turf, so they hunt as many as possible.

One year the rainy season is late, where the lions are, and early further noth, so the antelopes pass through there instead. The lions starve because they failed to trail their prey around throuout the year. Did the antilopes just commit planned extinction?

In my opinion no. There's thousands of factors that contribute to a species survival in the wild, many of wich change arbitrairily, like the weather. Noticing one surce of water makes you sick and avoiding that source if at all possible is not planned extinction, it's being smart. If another animals nieche get's taken away by the other animal changing it's behaviour it has to adapt.

(That's btw. how we got so many diffrent orchid/butterfly species in the rainforest, it was a war between the Orchids and a butterly that layed it's larva on it, destrying the orchids. The orchids responded by producing insectecide to protect themselves, and the butterfies developed immunities and so on...)

I am not in favor of planned extinction or most other kinds of forceful interjection with natural balance through humans, but that doesn't mean we have to deliberately let ourselves be wasted away in order to protect another species either. I say, as long as we dont use unfair advantage e.g. shooting every buffalo in sight, it's ok. After all we're an animal species on this planet too.

Bacteria/Viruses are a different story to conscious life forms like animals.

You have to be careful though because you might make it easier for more dangerous things, like MRSA.

And you might think i'm cruel/evil for saying this, but they help keep the human population down, we're overcrowded as it is. Nature will no doubt reduce us in number one way or another (or wipe us out).

Technically it's not a passive behaviour change though, it's a multi-million dollar international campaign with the goal of exterminating the worm.

Not that I disagree with doing so, but it's a bit different from the antelope scenario. It's planned.

To play Devil's Advocate, as small aquatic organisms, they are presumably preyed upon by things like fish or aquatic insect larvae. 

There are plenty of mutualist and commensalist symbiotic relationships between humans and other organisms (in all domains.) In fact they exceed the parasitic symbiotic relationships between humans and other organisms. So I really don't see why any "organisms" capable of sentient thought would think this. 

Secondly, how do we define, "higher organisms", biologically? There is no such thing. Humans are not higher than any other organisms, nor will any organism be higher than humans. Ethically we can make a claim, but ethical views vary and are not objective assessments.