要在msdb中部署多个SSIS包而不使用远程桌面，可以使用SQL Server Integration Services (SSIS) API来实现。以下是一个使用C#代码示例的解决方案：

using Microsoft.SqlServer.Management.IntegrationServices;
using System;

class Program
{
    static void Main()
    {
        // 设置SSIS服务器连接字符串
        string ssisServerName = "localhost";
        string ssisCatalogName = "SSISDB";
        string ssisConnectionString = $"Data Source={ssisServerName};Initial Catalog={ssisCatalogName};Integrated Security=SSPI;";

        // 创建SSIS服务器对象
        IntegrationServices ssisServer = new IntegrationServices(new Microsoft.SqlServer.Management.Common.SqlConnectionInfo(ssisConnectionString));

        // 部署第一个SSIS包
        string projectPath1 = @"C:\SSISProjects\Project1.ispac";
        string folderName1 = "Folder1";
        string projectName1 = "Project1";
        string environmentName1 = "Environment1";
        DeployProject(ssisServer, projectPath1, folderName1, projectName1, environmentName1);

        // 部署第二个SSIS包
        string projectPath2 = @"C:\SSISProjects\Project2.ispac";
        string folderName2 = "Folder2";
        string projectName2 = "Project2";
        string environmentName2 = "Environment2";
        DeployProject(ssisServer, projectPath2, folderName2, projectName2, environmentName2);
    }

    static void DeployProject(IntegrationServices ssisServer, string projectPath, string folderName, string projectName, string environmentName)
    {
        // 获取SSIS目录
        Catalog catalog = ssisServer.Catalogs["SSISDB"];

        // 创建文件夹
        if (!catalog.Folders.Contains(folderName))
        {
            catalog.Folders.Add(folderName);
        }

        // 创建项目
        ProjectInfo project = new ProjectInfo(catalog, projectName, folderName, projectPath, null);

        // 部署项目
        catalog.DeployProject(project, projectName, folderName, environmentName);
    }
}

上述代码示例使用了SSIS API来连接到SSIS服务器，创建文件夹，部署SSIS项目。你需要将项目的路径、文件夹名称、项目名称和环境名称替换为实际的值。

请确保已在项目中引用以下程序集：

• Microsoft.SqlServer.Management.IntegrationServices
• Microsoft.SqlServer.Management.Common