Disabling options on the Input Manager

You can set which aspect ratios are shown on that list (4:3, 16:10, 16:9, "Other"). I don't know what will happen if you disable all of them though... the user might not be able to select a resolution in the first place.

You can also, if I recall correctly, set the resolution of the game from within the game itself, using code.

http://unity3d.com/support/documentation/ScriptReference/Screen.SetResolution.html

So, theoretically, you could disable all resolutions via the Quality Settings options, and then create your own resolution options dialog within your game.