Just tested yesterday. The easiest way to unroot the HTC Magic back to stock is by just extracting the rom.zip file from the RUU_Sapphire_HTC_Asia_WWE_2.53.707.2_SEA_test_signed_NoDriver.exe.
Just run the RUU update and navigate to your %temp% folder and you should see there is 2 folder in {#numeric}, browse the folder and look for rom.zip
Copy it out and rename it to SAPPIMG.zip and put into your goldcard and update it to your Magic and it should now revert to the Pre Sense Android 1.5 with Engineering SPL
Once the phone booted up you can just plugin back to your pc and let the windows install the driver (HTC Sync driver , not Android SDK Usb driver) and you can just run the official RUU update and it should be back to stock room :)
** just make sure you are on an engineering SPL **