Your post accurately describes the trade offs. Personnaly, I would put all the data tables in a single file and then put all the interface elements, (layouts, scripts, etc) in a second file. That leaves you with just two files and most updates will simply require swapping out the old interface file for new without having to import any data. The assumption this approach is built on is that most updates update the interface rather than the structure of your tables.
Also, make sure you have downloaded the most recent update for your server software version as they may patch a bug that is causing your excessive CPU load.