Well. Poleski - not sure I totally understand the question but I'll offer this. If a squirrel isn't visibly sick (emaciated - visible sores or tumors) it's probably safe to eat. I know a lot of people put stock in checking the liver on rabbits. But, in truth as long as you cook your meat past 165 degrees there's very little chance of contracting anything from eating game. (Cook bear meat *done*)
You would be more likely to pick something up while dressing squirrels/rabbits/ etc. Many people use rubber gloves and it's probably a good idea, though, I haven't for the past 50 years and probably never will.
As I've stated before, I guess I'll feel lucky if it's a squirrel kills me. Only thing better would be a 25 year old jealous husband.
ballistic - I've never eaten the brains but know some who do. Don't guess I'll start with the connection to Mad Cow in KY. Besides that - I don't plan for the brains to be in very good shape when I'm done.