I suggest you to choose SSIS Package because SSIS is meant for such tasks. Well, for accessing file from other/remote server , you can use .NET Impersonation. It gives you a "Run As" capability in your code. If you Google you will find cut & paste code that you use with SSIS script.Using .NET bilkupload/Bulkcopy is not bad but using SSIS is right choice.
In SSIS " Script Task" you can write simple logic for column differences and make it work"
Shabir Hakim, Dec 20, 2014