So far I've been unable find a way of automatically accepting the EULA (short of using WSUS).
I then considered how to fool Windows into thinking the latest version of the Malicious Software Removal Tool (MRT) is already installed. I discovered this can be done by tweaking the MRT's Version key in the registry, so that it has the latest month's GUID.
I got the latest month's GUID from the following Microsoft page (Q2 under the FAQ heading):
Deployment of the Microsoft Windows Malicious Software Removal Tool in an enterprise environment
I updated the registry for this month (March 2010) and now Windows won't nag until next month when I can repeat this process again:
reg add \HKLM\Software\Microsoft\RemovalTools\MRT\ /v Version /t REG_SZ /d 076DF31D-E151-4CC3-8E0A-7A21E35CF679