Simpler is better IMO.
I would vote to have 1 Program in Marketo and 1 Campaign in Salesforce. In your Send Email outbound campaign, you could just use the Add Choice functionality to send 3 different emails based on certain criteria.
The thought of having 3 separate Campaigns in Salesforce for 1 singular Marketing effort doesn't make sense for me - you would never have multiple Campaigns for 1 Webinar just because some people who register for the webinar have a C-Level title and others are Students.