If an attacker can execute code through other attack vectors (JavaScript, Flash, or whatever), and happens to execute Java, instead of say native code, or batch

If an attacker can execute code through other attack vectors (JavaScript, Flash, or whatever), and happens to execute Java, instead of say native code, or batch files, or something else, that's not a problem with Java, it's a problem with those programs that have the vulnerability. The only way to be safe is to take your computer, encase it in a brick of cement, and drop it in the Mariana Trench. NoScript and careful browsing habits go a long way, though.