There are plugins for Joomla that can resize the images (can't think of the name of the top of my head at the moment) but you can also "resize" by setting the height/width via css.
I am not totally following your statement:
Sadly the upload script only seems to run when the image is uploaded.
It seems like there is more meaning behind that than I can read into it...
In any case, whether you upload an image or point to one, you can make it conform to whatever size you specify in the CSS and/or in the template itself.