RemoveRuntimeNode.cs

using System.IO;
using System.Linq;
using System.Xml.Linq;
using Microsoft.Build.Utilities;

public class RemoveRuntimeNode : Task
{
    public string ConfigFilePath { get; set; }

    public override bool Execute()
    {
        var doc = XDocument.Load(this.ConfigFilePath);

        if (doc == null) return false;

        doc.Root.Nodes().OfType<XElement>().FirstOrDefault(e => e.Name.LocalName == "runtime")?.Remove();

        using (var stream = new StreamWriter(this.ConfigFilePath))
        {
            doc.Save(stream);
        }

        return true;
    }
}