EDIT: Updated as my original answer didn't work and caused the build
to blow up. have now suggested to create a zip package, but to not
actually deploy the web application. Same Idea different implementation
Add dummy build.pubxml file to each of the unwanted projects and set them to not publish, but to generate a package, will work and not automatically publish the site.
<?xml version="1.0" encoding="utf-8"?>
<!--
This file is used by the publish/package process of your Web project. You can customize the behavior of this process
by editing this MSBuild file. In order to learn more about this please visit http://go.microsoft.com/fwlink/?LinkID=208121.
-->
<Project ToolsVersion="4.0" xmlns="http://schemas.microsoft.com/developer/msbuild/2003">
<PropertyGroup>
<WebPublishMethod>Package</WebPublishMethod>
<LastUsedBuildConfiguration>Release</LastUsedBuildConfiguration>
<LastUsedPlatform>Any CPU</LastUsedPlatform>
<SiteUrlToLaunchAfterPublish />
<LaunchSiteAfterPublish>False</LaunchSiteAfterPublish>
<ExcludeApp_Data>True</ExcludeApp_Data>
<DesktopBuildPackageLocation>Webapplication2.zip</DesktopBuildPackageLocation>
<PackageAsSingleFile>true</PackageAsSingleFile>
<DeployIisAppPath>webapplication2</DeployIisAppPath>
<PublishDatabaseSettings>
<Objects xmlns="" />
</PublishDatabaseSettings>
</PropertyGroup>
</Project>
This should allow the build to find a publishing profile, Create a zip file for the unwanted web apps but not actually deploy them.