Hi Ivan,
the option “Remove Legacy Agent” can be activated by appending WIXUI_REMOVELEGACY= to the msiexec command. Like this:
msiexec /i check-mk-agent.msi /qn WIXUI_REMOVELEGACY=
If somebody would want to disable the default option “Migrate from Legacy Windows Agent” you would have to append WIXUI_MIGRATELEGACY="".
msiexec /i check-mk-agent.msi /qn WIXUI_MIGRATELEGACY=""
I will try to find the time this afternoon to add this to our official guide.