Dear velnias2008,
Yes, turning off the Silverlight is not a big issue for you.
Search the following line in your project:
<ce:uploader id="InputFile" runat="server"></ce:uploader>
Change it to
<ce:uploader id="InputFile" MultipleFilesUpload=false runat="server"></ce:uploader>
It will disable the multiple files upload in CuteEditor for .NET
Thanks for asking
Eric@cutesoft.net