Plenty of electronic flight assistant devices are used on aircraft and I'm pretty certain a lot of them use Excel or similar programs.
Perhaps it is the way you are using the Excel spreadsheet? What safety checks are written in to constrain errors? Is the correct aircraft type displayed? Are the correct formulae inserted for each type of aircraft and suitably protected from being overwritten or altered accidently?
Anyone can write a simple spreadsheet to do load and balance calculations for multiple aircraft. Not everyone can write a speadsheet that protects the user from selecting the wrong aircraft type, errors in data entry or errors in the program itself. You need two or more independent checks (or calculation paths) built into the program to highlight any data entry or calculation errors.
I suspect the CAA are concerned that using a single spreadsheet to cover multiple aircraft introduces too many risks, and not that you can't produce loading sheets electronically. You just can't do it the way you have been doing it up to now because of some identified risk in the procedure they inspected.