Its so easy, just 3 lines of code. What you need is to reference mono.cecil.dll (google it!)
and:
var targetasmdef = AssemblyFactory.GetAssembly("My.dll");
//May seach for the one you need
targetasmdef.MainModule.Resources.RemoveAt(0);
AssemblyFactory.SaveAssembly(targetasmdef, "My2.dll");