BizTalk Server 2010 MP makes a lot of noise alerts and many SCOM Administrator decide to remove it as soon as they implement it but now there is a cure for this. The cure is provided by Bob Cornelissen who is well respected MVP. He created override MP and you can download it from here:
http://www.bictt.com/blogs/bictt.php/2012/04/12/scom-biztalk-2010-noise-reduction
Keep in mind the the MP by Bob still requires the original BizTalk Server 2010 MP.
Many thanks to Bob for providing this solution to the community.