There's a lot that is not understood about autoimmunity. I don't think what you're suggesting occurs in real life to any significant degree but it's not a crazy notion.

If someone had an autoimmune response to a particular protein and that protein happened to be very similar in structure to a viral or cancer antigen, they might have less chance of getting that particular infection or cancer.

The issue is that the "army" you're talking about is typically highly specific. It's not a "kill anything that moves" type of army. It's more like a "kill only troops that are carrying a sign that says, 'I am target S9p4kLwe43'". Literally, the immune system kills cells that present a highly specific and recognizable target on their surface.