Not sure if I was dreaming that I had the read-only working or what, and I doubt that this is the best way, but here is how I was finally able to do it:
...
doc.LoadXml(CreateXmaData(XDocument.Parse(xfa.DomDocument.InnerXml)));
PdfAction readOnlyAction = PdfAction
.JavaScript(MakeReadOnly(xfa.DomDocument.InnerXml), stamper.Writer);
stamper.Writer.AddJavaScript(readOnlyAction);
xfa.DomDocument = doc;
...
private string MakeReadOnly(string xml)
{
string formName = string.Empty;
int subFormStart = xml.IndexOf("<subform", 0);
if (subFormStart > -1)
{
int nameTagStart = xml.IndexOf("name", subFormStart);
int nameStart = xml.IndexOf("\"", nameTagStart);
int nameEnd = xml.IndexOf("\"", nameStart + 1);
formName = xml.Substring(nameStart + 1, (nameEnd - nameStart) - 1);
}
string readOnlyFunction = "ProcessAllFields(xfa.form." + formName + ");";
readOnlyFunction += "function ProcessAllFields(oNode) {";
readOnlyFunction += " if (oNode.className == \"exclGroup\" || oNode.className == \"subform\" || oNode.className == \"subformSet\" || oNode.className == \"area\") { ";
readOnlyFunction += " for (var i = 0; i < oNode.nodes.length; i++) {";
readOnlyFunction += " var oChildNode = oNode.nodes.item(i); ProcessAllFields(oChildNode);";
readOnlyFunction += " }";
readOnlyFunction += " } else if (oNode.className == \"field\") {";
readOnlyFunction += " oNode.access = \"readOnly\"";
readOnlyFunction += " }";
readOnlyFunction += "}";
return readOnlyFunction;
}