I am a bit surprised that this is seen as effective.
The rush costs 500 and is beaten by normal early raider defence and moving your commander. As in you could have some turrets which will deal some damage. If you have a construction it can make a defender to do some damage. If the transport attempts to collect your commander and the commander moves, it's weapon will kill the transport.
But I would like to retain enemy unit transporting. Not for the ability to early game commnap as I'm pretty sure that cannot be done as a normal rush, sure you may be able to do it with many people cooperating but that's a case of one team using teamwork and the other not.
Anyway I would like to keep transporting enemy units for the creativity. There is always EMPing an opponents force and stealing key units. Or for example you could defeat a lone Jugglenaut by spamming cloggers at it to bump and slow it down leaving several transports free to swoop in and capture it. I don't know all the possibilities but a large part of the game design is creating a lot of room for possibilities such as these.
So I think the issue is new people not knowing how to respond, which is an issue. It is sort of a issue with lots of possibilities, to not be suddenly killed players need to have a fair idea of the types of things that can be done.
A special exception is a problem for learning the possibilities in the long term. If things follow generally applicable rules you merely have to know the rules and you will be able to combine them and come up with creative solutions. With exceptions there is the extra burden of learning when the rules don't apply. For example someone could have a level 4 Rambo comm messing up their base, a spy and a transporter currently deal with this just like they would for other unsupported units.
So... in the end I'd rather just yet as it looks like a meta-game hiccup.