When we talk about balanced protection in a physical protection system (PPS), how do we consider countermeasures for intangible assets like intellectual property, brand value, company reputation, etc.?

Standard protections for intangibles still apply. For example, training employees to protect the organization’s reputation can assisted with  policies specifying employee’s online activities relating to the organization.  

For intellectual property you need to have access controls in place, data encryption, and actively monitor. You need a data map, data flow, and have the data tagged so you can do so effectively.

My two cents: First, I'd like to understand how big the problem is.  If the company is experiencing IP violations, incidents with brands, counterfeiting, negative publicity in social media impacting brands, etc.  Second, potential countermeasures would come as a results of the response to this assessment to include but not limited (if any), lessons learned from them and more important how to prevent them in the future; and if not (due to external factors out of your control), how to make your company less expose to these risks.