On Windows 64-bit system, disable/enable Java at system level will update registry, but only for either 32 or 64 only depending the JCP we use is 32 or 64 bit. The net effect is that, for example, if we disable 32-bit Java at system level, then 32-bit Java will be disable at both system and user levels, but 64 -bit will be disabled for current user only. If you switch to another user, then 64-bit is still enabled, which is nor appropriate because:
1. If user wants to disable Java at system level, then mostly likely what he wants is to disable all JREs, no matter if it's JRE8 orJRE7u, and no matter if it's 64-bit or 32 bit.
2. Even if we think 64-bit and 32-bit JRE should be disabled separately so current implementation at system level is correct. Then user level will become incorrect, because we disable Java for both 32-bit and 63-bit at user level at one go. And seems we don't non-trivial way to separate them because user level's deployment.properties file is shared for 32-bit and 64-bit Java, which controls whether Java is disabled at user level.

Also, this topic should have installation scearios involved. Say if we install 32-bit JRE and then disable it at system level. Then we install 64-bit JRE, IMO, 64-bit should also be disabled at system level. This is by nature the same scenarios as we install and disable JRE 7u10 at system level, then install JRE 8 - both JREs should be disabled.

Considering all above, the solution to me seems we should udpate both registry for 32-bit and 64-bit JRE, no matter if already have 32-bit or 64-bit JRE installed.