First of all, Sublime Text 2 uses two different files to control its appearance.
Color Schemes: A Sublime Text 2 colorscheme uses the same format as a Textmate theme. This misnomer causes a bit of confusion. Colorschemes only control the appearance of text in a view (and the background colors of course)
Themes: Sublime Text themes control the appearance of pretty much everything else. They affect the colors in the sidebar, file/replace panel, console, quickpanel, command palette, etc. Sublime has a default theme and there is also the popular Soda Theme.
Therefore, installing a textmate theme should not affect the appearance of the command palette.
To get this cleared up: where did you put the custom theme? It should be in "Color Scheme - Default"
What did you change in your settings file? You should have something like:
"color_scheme": "Packages/Color Scheme - Default/[NAME].tmTheme"