Well, as you said, people are being asked to pay to take part, so it seems a shame not to make the efforts to make everyone's games the best they can be. Trying to get GMs their preferred tables, not having lots of newbies at the same table and allowing people to play with people other than they normally do.
Like I said, I don't see it as a competition. But, as you're the event organiser, if you want strict "tournament" fairness, then I guess we do just that and shuffle players onto tables with indistinction.