One of the scenarios supported by the new Exchange 2007 MP (6.0.6623.0) is to keep the Exchange 2007 Converted MP (6.0.6461.0) installed. This allows you to keep your historical data from the old Exchange MP, while gaining the advantages of monitoring your Exchange 2007 servers with the new Management Pack. In order to do this you need to disable the monitoring from the old MP to avoid duplication of monitoring. This can be done with the attached unsealed management pack..
The management pack, Microsoft.Exchange.2007.Disable.xml, will disable all the rules and monitors in the converted Exchange 2007 MP. It uses enforced overrides to attempt to disable the monitoring even over any existing overrides you may have in your management group. Using this MP should avoid duplication of alerts, one raised by the old converted MP and one raised by the new MP and also avoid running the synthetic transactions from the old converted MP.
Edit: Updated the Attached MP, the version here was incorrect as it disabled the discoveries as well.