From what I've seen FMS11v3 is bundled with Java 6 u24. If you completely remove java it will prompt to install u24 upon the installation of FMS.
Keep in mind that Java updates come out much quicker than FileMaker Server updates. The installer your running for FMS may have been compiled over a year ago and will include an outdated version of Java.
The java version bundled with the installer is a known good working and tested version.
Sorry, but that's not the problem.
the FM installation do not continue if you do not accept the Java installation, so you are forced to install the old version of Java
so the process should be either:
or check the Java version already installed (if there is one) and if it is higher, do not install Java
or prompt the user if he wants to install Java, explicating with version is going to install