sorie6,
It sounds like the seedlings are coming up in a spot you don't want. Yes you can pot them for the fall swap. Conifers don't like to be disturbed when they are breaking bud. That's when the new growth tips (candles) break out into new soft growth. You can transplant before bud break or after the new growth has hardened off. I think one gallon nursery pots would be a good size, but it depends on the root system they have. I'm wondering if the roots might be intwined with the momma tree, but hopefully not at that small size. If your pots are black I'd either cover or paint them in a lighter color as black pots get very hot in summer sun. You could bury the pots in soil up to the neck so that wouldn't be a problem.
I would love to take one off your hands! It would be good to id the tree so whoever gets them know where to site it, how wide and tall they'll get, etc. If you can post a pic of the momma tree sometime this summer I bet the folks here can id it for you.
Good luck!