I have since been able to modify the uninstall.js supplied with the 6.x SEPIC component so that it removes only the SEPIC component and not SEP itself. Appears to be working for that component. Still having the issue of SEP being removed when aexagentutil is run.
var shell = WScript.CreateObject( "WScript.Shell" );
var connectSepAgentDir = "ConnectSEPAgent";
var sepProductCodeRegKey = "HKLM\\Software\\Symantec\\Symantec Endpoint Protection\\SMC\\ProductCode";
var altirisAgentInstallPathRegKey = "HKLM\\Software\\Altiris\\Altiris Agent\\InstallDir";
var connectSepAgentRegKey = "HKLM\\SOFTWARE\\Altiris\\Altiris Agent\\Plugin Objects\\Agents\\ConnectSEPAgent\\";
// remove the ConnectSEP agent
var filesys = WScript.CreateObject( "Scripting.FileSystemObject" );
var altirisAgentInstallPath = shell.RegRead( altirisAgentInstallPathRegKey );
filesys.DeleteFolder( altirisAgentInstallPath + "\\..\\Agents\\" + connectSepAgentDir, true );
shell.RegDelete( connectSepAgentRegKey );