I added EntityFramework.Migrations (Beta 1) to an existing Code-First app that is going through some changes (for both migration capabilities and more fine-tuning of the tab
You must use custom SQL script in Up method for setting default value:
Sql("ALTER TABLE TableName ADD CONSTRAINT ConstraintName DEFAULT GETDATE() FOR ColumnName");
Setting default value in code allows only static values - no database level functions.
Anyway setting it in POCO constructor is correct way if you are going to use code first. Also if you want to set the value in the application for some special cases you cannot use a default value in the database because the default value in the database requires either DatabaseGeneratedOption.Identity or DatabaseGeneratedOption.Computed. Both these options allow setting the property only in the database.
Edit:
Since the product is still in development my answer is no longer valid. Check @gius answer for actual way to achieve this requirement by using defaultValueSql (it wasn't available in EF Migrations Beta 1 but was added in EF 4.3 Beta 1 which already includes migrations).