How do I prevent personal emails from going into my PipelineDeals account?

Unless you have a person profile within Pipeline for the person you've been emailing, there is no record stored in Pipeline. Your Email inbox is only visible to you, so any personal emails with people who are not in your Pipeline system as people will stay personal. 

Hover over the email in your inbox and click Ignore Sender. This will ignore emails from that person for the Email inbox in Pipeline, but you'll still get their emails on your standard email client.