We will include a blank.gif file in the next release so people can choose to have no logo if their skin includes the logo option. That is the easiest solution.
To change the appearance of the logo you need to use CSS. You can add custom CSS to your skin by creating a style-site.css file in the skin folder and putting your CSS there. The class on the logo itself is sitelogo so if you wanted to add style to it you would add the following the style-site.css file. Once you have created your style-site.css file, edit the style.config file and remove the comments from around the line calling style-site.css (note, in future releases of mojoPortal and mojoSkins the style-site.css line will not be commented out).
border: 1px solid purple; /* this is just an example */
To reset the Skin Version GUID, go to
Administration > Advanced Tools > Design Tools > Cache Tool and click the Reset Skin Version GUID button.
Hope this helps,