One of my webservers has postfix installed as satellite host (special config).

In ISPConfig Mail is set to no.

When I start the updater and say reconfigure services -> yes it detects postfix and reconfigures this even though it is set to no in server config.

In my opinion the already configured "no" shoud override automatic detection. And if you do not want that please consider asking if the user really wants this as detection differs from database settings.