Email Link Performance Report Question... How do you differentiate on the CTR report if it was a regular person or a mail scanner system checking links on the way in?

How can we determine if the clicks/leads are real people or email scanners?

You cannot. There is no way within Marketo to accurately distinguish between modern anti-spam/anti-abuse scanners and human clicks.

Also, how can we then check to see if someone actually followed through on the Call to Action they clicked on?

Well, that would be another action (Filled Out Form, etc.). If it always requires human interaction (choosing to click a button/navigate on a web page) it could be reliably attributed to a human end user.