C# would access MySQL and SQLServer basically identically using ADO.NET (or LINQ - LINQ to SQL is tied to SQL Server, but it doesn't appear to have a long life ahead of it), so that wouldn't be a factor in my mind, although IDE integration might be.
The benefits of SQL Server would include the more complete gamut of development support within SQL Server, the Agent and scheduling, the security model, and indexing, tuning and other features like Integration Services, Reporting Services and Analysis Services which make it relatively easy to manage large system infrastructures.
I don't think you've given enough information about your system to make the choice between them obvious at this point.
