I think it would be too much hassle to get this to happen. My advice would be to pick the fx cop rules that you can live with, and get all the errors/warnings out of your code. That way if another team member changes something, you will spot it, unless they are writing code that passes. in which case there is no problem.
Unless you are working on some masive project that takes ages to check with fxcop, I think this should be ok and there is no reason to only check incremental changes.
If you are in a situation where a project has got so big that it takes ages to analyse, consider refactoring. In a Visual Studio context, wherever you have folders in a project, consider making them into new projects. This will help with separation in your code, and make it possible to analyse parts of the whole solution, rather than the whole solution and all it's projects, most of which will have no changes.
Refactoring will often be quicker, with less of a learning curve, than making a really customised testing setup to compensate for a difficult scenario.