Here is the steps for this:
1) Disable the organisation that you do not want to upgrade.
2) Apply the roll up / service pack to rest of the organisation.
3) Enable the organisation that you do not want to upgrade. At this time, system will ask that there are new rollups available, do you want to upgrade. Select No for this.
There you go. You have same server and multiple organisations on different roll ups. This is what deployment administrator console shows.
Hope this helps