You can use MQSeries to push data to, and get data from, the mainframe. What you're doing with COBOL could best be accomplished with BizTalk and Host Integration Server (HIS) together. HIS 2006 (included with the BizTalk 2006 license) allows you to convert COBOL and RPG source to XML schemas (using the Transaction Integrator plug-in for Visual Studio that comes with HIS).
Check out http://www.microsoft.com/hiserver/default.mspx for more on HIS. They key is, HIS 2006 ships with BizTalk adapters for MQSeries, DB2, host data files, and host apps. So, you can use BizTalk to route and validate data, and use HIS to interact with the mainframe.