How are you currently deploying?
If you are managing this via ePO, I dont see a product update or product deployment task that you can configure to just remove the patch. (I am assuming you are moving from 8.8 Unpatched and applying Patch 1.)
Hotfixes can not be removed in any case. Patches can be removed manually, the readme for the Patch will include instructiions on how to do this. You have to uninstall/reinstall VSE if you want "uninstall" a hotfix. In your case it might make sense to apply the respective updates to a small subset of machines first (IT, test group) to check how the updates interact with your inhouse applications/everyday tools etc.
Based on the testing you can then decide whether to roll it out to the whole enterprise or make some more tweaks to the configuration etc.