There is no way to prevent JuiceboxBuilder-Pro from creating the .tempGallery folder (which is integral to JuiceboxBuilder-Pro functioning correctly).

There must be a reason JuiceboxBuilder-Pro beign unable to delete the .tempGallery folder when the application closes and it sounds like it might be a permissions issue.

First of all, try manually deleting the C:\Users\Username\Documents\JuiceboxBuilder-Pro folder itself.
JuiceboxBuilder-Pro will create a new one on next run and it might be set up with permissions that not longer cause your problem.

If this does not work, then navigate to your C:\Users\Username\Documents folder, right-click the 'JuiceboxBuilder-Pro' folder, click 'Properties' at the foot of the context menu, go to the 'Security' tab and see if there are any ticks in the 'Deny' column in the 'Permissions' box for any of the groups or user names.
For my own installation (with default settings), there are ticks in all the 'Allow' chekboxes (except for 'Special permissions').
If the permissions for your own 'JuiceboxBuilder-Pro' folder are not set up like this, then try changing them to see if this makes a difference.

I hope this helps.

It can't hurt to try.

A couple of other things to consider...

(1) Have you ever saved or tried to load a gallery in JuiceboxBuilder-Pro from a folder that is actively being synced with an online file sharing service such as Google Drive or Dropbox? This has been known to cause a persistent .tempGallery folder which JuiceboxBuilder-Pro cannot delete.

(2) Do you have any third-party security software installed (such as an anti-virus program or malware protection) which might somehow be interfering with the functionality of JuiceboxBuilder-Pro? If so, then try temporarily disabling it to see if this helps to resolve the problem.

Unfortunately, I cannot explain why JuiceboxBuilder-Pro is unable to delete the .tempGallery folder when using your E:/ drive but at least you now know the cause of your problem and can work around it.

I've just tried using a test gallery on an external drive (labelled E:/) on my own computer (admittedly not exactly the same as your scenario but the closest I can get) and it works fine. JuiceboxBuilder-Pro successfully deletes the .tempGallery folder each time the application is closed.

I can't help but think that the problem is a permissions or file ownership issue.
If you are using a Windows PC, then try uninstalling and then reinstalling both JuiceboxBuilder-Pro and Adobe AIR but when you reinstall Adobe AIR, rather than just double-clicking the 'AdobeAirInstaller.exe' installation file, try right-clicking it and selecting 'Run as administrator'. This might help.

At least you have a workaround. Saving the gallery to your C:/ drive and then copying it to your E:/ drive might be inconvenient and an extra step in your workflow but at least it works and it might be a slightly easer option than manually deleting the .tempGallery folder each time you use the application.