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This is an all too common scenario within the corporate world. I have to deal with exactly this problem and it isn't easy. The apps are business critical and cannot be replaced (last replacement implementation project came in at $15 million). There are firewalls and other layers of protection, but these are PCs used by staff who will also surf the web and ...
It sounds like you are in a corporate environment with in house or vendor specific applications needed for business. You should be able to use a combination of code signing and whitelisting to setup policies where it will only run the JAVA applets and applications that are authorized. This is not full proof, but may help to reduce infections. See the JAVA ...
Are the machines internet facing? If it is, you are screwed. If the machines are not internet facing, keeping them behind a firewall with very strict access conditions might reduce the possible attack surface enough. There is no true alternative to simply patching or removing Java though.
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