Until we develop our own ATUM API end-points planned for later this year, this data is not exposed. So actually, you cannot do that through the WooCommerce API.
However, I'm thinking a possible solution that could work for you now in the meantime. It's an advanced solution but if you are a developer, you should know how to do it:
I'd continue creating the _purchase_price post meta the same way you were doing through WC API and I'd add a hook triggering after a product is updated (for example in woocommerce_update_product). And once this hook is triggered, if the post_meta for that product exists, I'd update the atum_product_data table with the current value and would remove the _purchase_price post_meta to not trigger again.
I hope this helps.