iCloud is a sync solution, not a backup solution. Deleting from one device deletes from all, by design.
If you used two separate IDs, they would not sync at all. Each would be completely independent.
If you don’t want syncing, you’d be best to disable it rather than attempt to use two separate IDs.
System Prefs > iCloud > iCloud Drive > Options…
Disable everything except essentials like Contacts etc.
As it’s a structure I’ve never used, precisely because I don’t want the same data on all machines, I don’t know what warnings you will get if you disable. Make sure at least one machine keeps the original data & make sure Time Machine is up to date.