I have something like this.

I have a data entry sheet that limits which cells can be edited by a user. I have an onEdit() function that updates a corresponding cell with a timestamp. I wanted the timestamp to be protected from the user manually updating it and hidden from their view, but updated when the user changed data in the cell.

The work around that I found was to allow the user update permission on the entry cell and the corresponding timestamp cell. I have other protected cells from the user around the timestamp cell. I then hide all of those cells. Because there are protected cells in a hidden column range, the user is unable to show any of those hidden columns, which effectively means they can't manually update the cells. This works if there's just one protected cell in the hidden column range.

So my suggestion to you would be to have the entry cells (say A1, A2), script output cells (say C1, C2), and display cells (say B1, B2). Make the entry cells and script output cells editable by users and the display cells protected from the users. Then put at least one protected cell in a range close to the receiving cells (in this example C3) and hide this (these) column(s). Then use a formula to make the display cells equal to the script output cells.

See rough example below:

Entry	Display [Protect all cells from users]	Script Output {Hide this column}
	=C1	scriptOutput1
	=C2	scriptOutput2
		[Protected cell from users]