If you use a siphon, you can avoid crushing his bubble next by placing a half Styrofoam cup in the water for him to build inside.
You'll do a lot less damage to the nest.
But just because a betta is making a next doesn't mean you have to breed him. It just means he's healthy. You should do a lot of research before breeding. I would find your girl her own aquarium. Something 2.5 gallons or larger, preferably. And keep her tank away from the male, so they don't stress each other out.