Hi Viktor,
As you mention in your question, you will need to use Custom Service Node types for doing interactions. Try to avoid using script nodes. Custom Service Nodes are implemented creating new implementations of the WorkItemHandler interface. Those implementations will interact with your external systems. If those interactions are Syncrhonous, jBPM will behave in the same way that your old framework does.
Regarding the operations with the DB which seems to be transactional, it depends on how do you want to do it. If you start a transaction against your DB inside a workItemHandler and then write the logic to see if everything else went right and commit that transaction, everythhing should work. Notice that for what you describe, you don't need to persist your "Flows" because all what you need is to execute the steps and commit or rollback the information to another external database.
Cheers