EVALUATION

This is an approach to fix the bug (currently being revied by Java Installer team):

Registry.idt creates during build process registry entry templates in installation bundle
(i.e for example in jre-6u12-windows-i586-p.exe )
When installation bundle runs it creates msi file and puts these registry entries templates to it.
When msiexec.exe executes msi  file  it  creates a  real windows  registries based on
entry templates (originating from Registry.idt) and on predefined msi properties like  for  example
[JDK_VERSION]  or [MODE]

There is a way to pass additional properties (or modify values of existing ones) to msi
by specifying them in command line parameter while running either a wrapper:
 jre-6u12-windows-i586-p.exe  PROPERTY_NAME=VALUE
or
msiexec.exe /i jre1.6.0_12.msi  PROPERTY_NAME=VALUE

So if  I run
jre-6u12-windows-i586-p.exe UNREGJQS=1
then UNREGJQS propert will be accessible by Regutils.dll
by running
BOOL FindMSIProperty(LPCTSTR lpszVersion, LPCTSTR lpszProperty, LPTSTR lpszPropertyValue, DWORD dwCount, const int installType, LPTSTR lpszAltPropertyValue)
function
defined in RegInstall.cpp

and as a result if I check UNREGJQS in InstallJQS() function in regUtill.dll I will be able to decide wherever to start or not JQS service.