Munnin,
For a basic, first-principles approach, I've successfully used the following procedure:
1. Neglect vehicle crush, boulder spalling, etc.
2. Assume a fully plastic collision.
3. Use Conservation of Momentum to determine post-collision velocity of the vehicle-boulder system.
4. Determine post-impact kinetic energy of vehicle-boulder system based on velocity obtained in 3, above.
5. Estimate friction coefficient between boulder and ground. This can be tricky... be conservative.
6. Determine stopping distance using Work-Energy Principle.
The maximum allowable stopping distance may be governed by the AHJ (authority having jurisdiction), depending on which agency it is. Otherwise you (or the security consultant, if there is one) will need to determine if the penetration distance is acceptable based on your site-specific requirements (e.g. required standoff distance). As you mentioned, you can increase the resistance of the boulder by partially embedding it; this will add soil mass/passive resistance to the Momentum and Energy considerations.
Hope this helps.
Brandon