You can still do a pretty similar experiment. For instance, startups 1-50 get into yc like normal. Startups 51-100, together with 50 randomly selected startups get grouped together and tagged as "the bubble group". Meaning that they were on the bubble of getting into yc. Pretty high honors. However, they don't get any access, consultation, etc. to yc itself. Then after a few months you unblind which were highly selected and which were random, to see who does better.

You could also accept groups with good interviews in the experiment batch, but not include them in the experiment.

We would only be able to conclude that it's unfair for "great start ups" if the experiment showed that random acceptances performed worse than the interview process.