You can of course set up your points structure however you want. If you want to subtract a bunch of points for someone doing a rebuy you can easily set this up in your points formula
I just have my formula set up to subtract a single point for a rebuy, so there is some point "punishment" for rebuying, but in my view, if you allow a rebuy then that is part of the strategy of the tournament and someone shouldn't be set back to middle position for doing something that is part of the established structure of the tourney. One of the advantages of a rebuy is also to get more money in the pot, so you may not want to discourage people rebuying.
My points formula is essentially a number of players minus rank, with a couple bonus points for finishing top 3. So, in a 20 person tourney the winner will get around 23 points. So the loss of a single point doesn't mean that much, but over the season, the loss of points through rebuys can affect the season winner.
Another way to "punish" a rebuying player is to only allow a "short-rebuy". I also use this as part of my tourney structure.
I do 2000 chip buy-in tourneys (for say $20). Then if someone rebuys, they can only get 1500 chips (for a discounted price of $15). I like this approach because then the person rebuying is relatively short-stacked, but still can play a good bit longer and may even make a comeback depending on what level they rebuy at (I allow a single rebuy through 1st 3 rounds).
FWIW