The only way to really tell would be to take a piece of the unaltered soundtrack and compare it to the altered version, and even that might not yield much. But then, even with the free editing software available online, you'd be able to find out if there's any difference in the speed, even an otherwise neglible difference.
If it were my call, though, I'd opt for whatever option didn't involve playing with the speed, if only to simplify the editing process. The only objective in this aspect was to make it sound not
like Malachi Throne, regardless of whatever the final sound was. And I've heard the whole thing unaltered, when Roddenberry played "The Cage" at one of this lecture stops, and I seriously doubt they did anything that changed the playback speed, even minutely.
I think they ran it through something to take out the lower range and fuzz it up a bit (maybe a Fender amp, maybe even a Fender guitar -- think Aerosmith's "Sweet Emotion" or a typical old school Cylon, only not as intense), so that matching up with the original footage wouldn't even be an issue.