Good point. I'd always figured that chakra could help kick out infection. Otherwise, healing a cut could go disastariously wrong.

Exactly. No point in healing a wound if you're going to trap in a bacterial infection.

I have a pet theory (absolutely no basis in canon, but I think it'd be cool) that chakra messes with the immune system: it fights infections and pathogens and regulates immuno-response so that allergies are rare. The downside would be that what gets by it would be pretty devastating and impossible to treat (like those multi-drug resistant strains of TB), and that if someone did develop an allergy it would likely be fatal.