We have a similar situation at my company, although, we have also had the happy coincidence that the different portals are not used by the same individuals. Therefore, even though Java 8 is the corporate standard, a few customers have been downgraded to Java 7, and a few others have been downgraded to a very specific version of Java 6.
This truly is a nightmare scenario, especially when certain vendors are unable or unwilling to update their software.
Now, as a developer, I have to switch between all the portals and their version requirements. And...
Unfortunately, I am sorry to tell you there is no known "customer friendly" way to switch between Java versions for browser applets. You must go into the Java control panel, activate the JRE that you need, and deactivate all the others. (Some of our customers are Power Users and can handle these instructions. Others want it to "just work" and unfortunately, this kind of thing does not just work. I dealy hope you are able to find a good solution for your customers who fall into this latter category.)