Yes it can.  Ideally, you would have your SEPM at MP3 as well, but it can manage small amounts of MP3 clients if it is still at MP2 with little or no noticeable issues.

You'll want to add the MP3 installs to the MP2 SEPM and create an exported package so these MP3 clients will check in.  Or just upgrade by adding MP3 install to a group.

Here are instructions:

Creating a new package within SEPM:

1. Open Symantec Endpoint Protection Manager console
2. Click the Admin Tab on the left
3. Select the Install Packages button in the lower center section.
4. Click Add a Client Install Package under Tasks
5. Specify the name you would like the package to have
6. Click Browse
7. Browse to the location where your RU6 MP3 media is