How can an obstruction of justice claim hold any power if the individual is found to be innocent?

It's not entirely clear what you're asking.  You seem to be asking how someone could be charged with obstruction of justice if there is no underlying crime which they are guilty of. 

The law says that there doesn't have to be an underlying crime for obstruction to take place.  There's very good reasons for this.  If a person could only be charged for an investigation which resulted in their conviction then there's effectively an incentive to try and obstruct justice, since if you do it successfully you can't be charged.  Let's give a hypothetical example to show what I mean.  Let's say I'm charged with some crime (what it is doesn't matter).  I go to trial and get acquitted.  Then, after the trial it's discovered that I bribed the jurors.  Under your preferred version of obstruction I could never be charged with anything because I am, under the law, innocent of the crime which I committed obstruction to interfere with.  We need to be able to charge people who have not been convicted of an underlying crime with obstruction in order to keep the system working.

It has been done. We are all presumed innocent, but may obstruct justice from misplaced emotion or loyalty.

Obstructing a lawful investigation costs the taxpayers money; thus obstruction is rightly considered a crime on its own.   In 2004, a typical year, federal agencies arrested 446 people for obstruction of justice, representing 0.3 percent of all federal arrests. This does not include, however, people who were charged with obstruction in addition to a more serious underlying crime.

In other words - don't troll the feds - they will not be amused and they might arrest you.

Are you referring to a particular case where a defendant was found to have obstructed justice AND was found innocent?

I've never heard of that happening before.

Wouldn't they be suspicious that he would have been found guilty if justice had been unobstructed?

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Obstruction of justice is a crime in and of itself. 

Obstructing justice prevents getting to the truth which can affect the end result. 

No one is ever found "innocent" in criminal court. Its guilty or not guilty. Not guilty and innocent are two different things. 

Obstruction of justice is an additional crime, not a crime you can commit by itself.  I have heard of only one case of someone being found guilty of obstruction of justice with no underlying crime and that was overturned. 

Because the law does not pardon them if they are found to be innocent. Same with people who resist arrest. Even if they're found innocent, that is a separate charge of its own. You cannot obstruct justice period. (and if you're innocent, why would you even)