It's best to just leave them be.. if you are properly prepared then taking care of 5 babies isn't any different than taking care of 50. As mentioned already, unless you disrupt the whole thing and risk losing all of them, you don't get many chances at removing her. Also, you are not guaranteed that the first clutch or two will be fertilized. He may pick them up and place them in the nest, but he is doing it when he *thinks* it's a good wrap and after they finish breeding he will then go through all the eggs, take out the ones not fertilized, etc. So you may end up with no eggs in which you will have to recondition for a week or so and try again later.
And there will be a small chance of her becoming egg bound as her eggs are ripe and needing released, but she just got stressed by being removed in the middle of their breeding where she was stunned (and usually out of sorts for a bit after spawning as well).. very slight risk of it, but it can happen - I lost one of my best breeders from egg binding because she couldn't get them released with the male as they were having issues wrapping so I had to remove them and she became egg bound.
I say let them breed.. see how many you get (you can get anywhere from 10 to 600+) and then cull as needed down the road once you see what you have - you may accidentally end up with all females or deformities that will cut the small number you keep down even more. So I say just let them do their thing and cull as needed afterwards so you can keep the better of the batch.