You could just remove the line:
$dialplan_xml .= " <action application=\"set\" data=\"presence_id=".$ivr_menu_extension."@".$_SESSION['domain_name']."\"/>\n";
from ivr_menu_edit.php, probably a similar one ivr_menu_copy.php
Only thing you'll have to be aware of is a possible conflict when you come to update the PBX, so because of this I've reported it to the FusionPBX lot to have a look over as a bug. Hopefully they'll add a flag to disable the monitoring of the IVR or work out what logic is needed to make it work.