You are actually better off putting up with .. whatever problem cleartype is causing you than to try and cut the UI apart. Even then, many many programs are designed expecting standard fonts and cleartype to be enabled, and sometimes trying to force-change these could break their ability to display their UI elements properly.
While there are some programs that are designed to use Segoe UI, I have yet to see one that looks bad when forced to Tahoma. That said, NoSegoe, the component in Windows Aero (Tahoma Font) that forces the replacement of Segoe UI in everything that isn't part of the Windows UI, is known to completely prevent some Adobe programs from running. To get them to work however, you simply need to run them in compatibility mode for XP SP3 or older. Of course this has already been mentioned in the Readme.
Though it is possible that there are other programs that will refuse to run without Segoe UI, they should also need nothing more than a compatibility mode setting. As such, I see no reason why a person shouldn't try Windows Aero (Tahoma Font) if they feel they need it. If worse comes to worst and a UI element in a program is displayed improperly, Windows Aero (Tahoma Font), or even just NoSegoe, can always be uninstalled.