Yes, you can encode to 1080p Smooth Streaming in Main Profile as follows:
The XMLs for all the presets are available via Getting Started Sample code (http://go.microsoft.com/fwlink/?linkid=253275), in the "WAMEPresetFiles" subfolder.
Open the "H264 Smooth Streaming 1080p.xml" file in a text/XML editor, and replace HighH264VideoProfile with MainH264VideoProfile. Save it, perhaps as "H264 Main Profile 1080p Smooth Streaming.xml"
Follow the steps in http://msdn.microsoft.com/en-us/library/windowsazure/dn296426.aspx that show how you can use File.ReadAllText() to load the contents of the above XML file to a string, and then use that string in an encode Task sent to Azure Media Encoder