This might be a long shot for you, but here's a potential solution based on the way my SNMP monitor works. I'll use examples from one of my Debian machines since it sounds like you're using Debian.
On a switch, there's a difference between a port being down (disconnected) and administratively down (disabled). I don't think the terminology is the same on servers, but the concept is.
For example, I have a network interface "enp2s0" with the following status. If I run "ifconfig" it appears, despite being physically disconnected.
If I run "ifconfig enp2s0 down", the interface no longer appears unless I use "ifconfig -a". To use switch terminology, this is the difference between being down and administratively down.
To keep the network interface administratively down after reboot, your /etc/network/interfaces entry should look like this:
Code:
iface eth1 inet manual
This should tell the Debian networking daemon to not automatically bring the interface up, but I haven't tested this. The also assumes you don't a GUI network manager superseding the configuration in your interfaces file.
In my SNMP monitor, this is what it takes to make it stop randomly notifying me that an interface is down. However, I don't use SNMPTRAP so this might not be useful to you at all.